May be two reasons:

1. Medicines tested on a set of population and used by another set of population with different environment and features.

2. These are artificially developed and processed chemicals/salts not natural.

Forgive me if it is wrong as I don't have medical background, I answered as layman.

All allopathic medicines are artificially created and the chemicals used are designed in such a way that they only cure the problem on the surface.

The same treatment is used for people with different, usually unknown, physiological characteristics?

Medication has been developped and tested in a biased group of the human population (e.g. only adult males assuming that women and children respond in the same way to the treatment?)?

Any substance ingested by humans can cause side effects. It is not true that "tea" or any infusion are harmless for being considered natural products. The key tip is to rely on the doctor's counseling when one does not feel well. The medical doctor will prescribe the best treatment and he will be able to adapt it according to one's reaction to the drug prescribed, if any is needed at that time.

May be two reasons:

1. Medicines tested on a set of population and used by another set of population with different environment and features.

2. These are artificially developed and processed chemicals/salts not natural.

Forgive me if it is wrong as I don't have medical background, I answered as layman.

There are some side effects may be caused by allopathic medications.

Side effects of allopathic medications vary wildly from mild to severe and there are many. They include insomnia, vomiting, fatigue, dry mouth, diarrhea, constipation, dizziness, suicidal thoughts, hostility, difficulty sitting still, depression, mania, seizures, coma, anemia, hair loss, high blood sugar, shoplifting, swelling, impotency, panic attacks, confusion, fainting and death.

It is often difficult for seniors to keep track of multiple medications which further increase likelihood of side effects due to allopathic medicines.

Allopathic thinking fosters the concept of "against." We must kill germs, kill viruses and kill bacteria. The reason these micro-organisms exist and our mutual relationship is ignored.

http://www.ehow.com/about_5655922_side-effects-allopathy.html

It is necessary to consume proper quantities of allopathic medications in order to avoid its side effects. The following forum discusses how to minimize side effects of allopathic medications: " MINIMISING THE SIDE EFFECTS OF ALLOPATHIC MEDICINES": All allopathic medicines are having side effects because of their method of preparation. Fortunately, there is sense prevailing with some companies and I have seen they are producing now medicines at least which have ethereal contents and ending in IN like Novalgin etc in drops with droppers attached to the bottle and asked to administer in drops diluted in water. This is a very welcome change. All substances and all living and non living have a medicinal and toxic part. In human being we call it paap and punya (the evil and righteous parts). The best solution for removing the evil part in a human being is to dilute it with love. If an evil person is given adequate love and affection, the possibility of his changing into a good person is more than if you beat him or punish him and try to correct him . Similarly, the toxic content in an seemingly inanimate substance can be removed at best by diluting it with the spirit called Water which is life giving. Water in its purest and pure forms are always and always life giving. So the life giving water has a capacity to remove the toxic injurious effects from any substance by dilution. This itself is the principle working in homeopathic dilutions to some extent. In the allopathic or conventional pharmacopoea they fail to remove this toxic part and therefore those toxic parts remain as side effects while the medicinal part does its function of suppression, blocking, or cure as the case may be. Since the natural process is not attempted by the allopathic medicines, their work is limited to blocking, suppression or repair works where the patient does not feel the sufferings for a period of time or the causative agent is blocked or stopped for a period of time in its assault and during this period the body gets the necessary respite to function with vigor and strength as it ought to be, and thus the body is able to remove the malady temperorarily or permanently. The allopaths call that cure. Whereas in homeopathy natural cure is attempted and therefore it is a metamorphosis or conversion for a state of morbidity to a state of health. The allopathic medicines does not achieve that subtlety because it is passing through the digestive system (which is level of Fire)normally or at the most through Intravenous injections which is level of blood, i.e. liquid or Element Water whereas the subtle levels at which homeo medicines function are Air level or Energy level of Ethereal levels. Ethereal levels are mind and beyond and therefore metaphysical. See more on the link:

www.homeopathyandmore.com/forum/viewtopic.php?p=48239&highlight=

 I think allopathic medicines contain some sort of artificially developed chemicals which may not fully processed by human body and causing some side effects.

Do artificially developed chemicals break down more slowly than natural chemicals therefore increasing the physiological impact time window therefore causing side effects?

Dear Marcel, I agree with you that some artificially developed chemicals break down slowly than natural chemicals and producing the side effects.

Allopathic medicines may be an unbalanced product. But other than that it is as natural as any other substance.

I wonder if there is a method to separate these substances the cause side effects from the allopathic medications?

Traditionally Allopathic medicines are artificial chemicals, which produces some harmful substances after breaking down.

If you review all the possible side effects of Amoxicillin, Amikacin, Meropenem, Azithromycin... you may favor "some" alternative medicine or opt for home remedies if possible!

The term "allopathic" medicine has its roots in the past, but is still used in a derogatory sense, the advocates of so-called natural or alternative medicine, although it has now seen undermines the very principle on which it was based following the enormous progress in terms of methods and scientific-medical criteria recorded during the twentieth century. In the medical scientific and experimental, in fact, it is not relevant that the treatment be similar or opposite to the disease that needs to heal. The only important thing is that the therapies and drugs "allopathic" function effectively, safe, reproducible and documented.

"The term "allopathy" was coined in 1842 by C.F.S. Hahnemann to designate the usual practice of medicine (allopathy) as opposed to homeopathy, the system of therapy that he founded based on the concept that disease can be treated with drugs (in minute doses) thought capable of producing the same symptoms in healthy people as the disease itself."

http://web.jhu.edu/prepro/health/allopathic.html

Dear @Abedallah, I think the harmful substances are the results of breakdown of main chemical, which cannot easily be separated.

Yes @Alireza, For avoiding the side effects of Allopathic medicines, we should definitely use alternative medicines including home remedies.

Dear @Enzo and dear @Nageswara thank you very much your detailed and useful comments on the topic.

Hypertension is bad, but hypertension drugs are worse. Blood pressure medications can cause heart failure with prolonged use. They all seem to have a pattern of side effects, which include heart and muscle damage, irregular or fast heart beat, restlessness, and light-headedness. Weaning off these drugs should be done slowly and cautiously, with frequent monitoring for dangerous spikes in blood pressure. Bear in mind that whenever weaning off of such drugs, one should expect sudden and temporary rises in blood pressure. This is temporary, and the instabilities should diminish in time.

http://healthwyze.org/index.php/component/content/article/469-the-big-one-naturally-preventing-and-curing-heart-disease.html?start=1

I think considering the negative side effects of  allopathic medicines, its better to use other alternative/natural treatments. Nevertheless, the natural/home remedies work quite slow as compared to allopathic medicines.

Allopathic treatment offers a material basis for disease and considers an ailments caused by a "thing' like bacteria, virus, etc or metabolic disorders. Other factors i.e. diet, nutrition, lifestyle, emotional disturbance or family problems tend to be de-emphasized or wholly ignored. Allopathic medicine uses treatments and medicines which produce symptoms that are different from symptoms of the disease. Allopathic view fosters the concept of ‘killing’ which is against. The purpose of taking allopathic medicine is to suppress the symptoms one is experiencing, not necessarily to cure, or heal the condition. Long term life regimens of drug taking are encouraged, which often leads to higher incidence of side effects. So far medications are concerned; these are chemicals – whether Synthetic or Natural. All chemicals have their own positive and/or negative impacts, it is the dose that matters. Allopathic drugs contain only those chemical(s) that have suppressive/killing effect against specific germ/virus or condition but it may cause undesirable impact on other organs/systems of the body. On the other hand, in plant based medications, the entire plant or part is taken that contain several other balancing chemicals in addition to the chemical required to cure the diseases. However, plant drugs if not prescribed with holistic approach and taken inappropriately, may also cause adverse side effects.

Yes, I agree that most of the allopathic medicines suppress the symptoms of the disease rather curing it and perhaps this is the reason of their having side effects.

Yes Brenda, You are right but we have to differentiate between allergy and serious side effects.

Dear Breenda, this is obvious that if someone is allergic to some natural products, s/he must avoid them.

Dear Prof Ajay Singh ji; in my opinion not only allopathic medications have side effect, infact homeopath and or other medicaton systems like unani etc can also have side effect. Thanks

Dear Dr. Dubey ji, Thank you for your comment. If you compare all the medications, allopathic medicines have far more negative side effects as compared to any other medicine systems. Of course excess of anything (even good) is bad.

Yes, Every drug whether Allopathic, Ayurvedic, Unani, etc depending on their chemical makeup exerts specific curative effects as well more or less after effects.  Medicines prescribed under Traditional or Alternative systems of therapy are prepared out of natural sources and being more nature-alike, they have very low or no after effects, if taken appropriately.   

I think most allopathic medicines have certain side effects even if they are taken in appropriate doses, i.e., simple painkillers could be very dangerous, if you use them regularly.

1. We must first try for natural medicines, if possible, as our body accepts very fast.

2. We should, if need be, take allopathic medicine only after recommendation and within prescribed dose.

3. Any medicine, may be nature based medicines or allopathic medicine, is foreign body to us and it may take to adjust with the body.

4. Try to prevent the disease by exercises, yoga, etc.

Yes, I fully agree that prevention is much better than cure and to avoid any possible side effects of medication, we should try natural ways and home remedies, first.

Dear Brenda, As I posted earlier on this thread that excess and inappropriate use of anything (even good) is bad. So, if you are allergic to something, you should not be using it whether it is natural or not.

Some people claim that a molecule penetrating the body might be divided into 40-50 different chemicals where different chemicals might act on different parts in the body. Perhaps where the compounds will act will differ between individuals?

Can it explain why a molecule like consumed alcohol can produce different exaggerated feelings between persons that consume alcohol? E.g. After alcohol consumption, some will be happy, others fall asleep, others become overexcited, others will become melancholic, etc.....  Is this because the chemical compounds that result from the breakdown of alcohol will end up in different parts of the body also expressing inter-individual variation?

Yes, Marcel; chemical compounds that result from the breakdown of a allopathic medicine may create many problems in different parts of the body with inter-individual variations in responses.

Allopathic care is lifesaving and an absolute must in emergencies or life-threatening situations.

http://www.alternativemedicine.com/alternative-medicine/less-medicine-best-medicine

Yes this is very true and obvious that we cannot think about home/natural treatments in medical emergencies because home remedies/natural treatments work at a very slow rate.

Natural treatments, e.g. herbs, consist of a cocktail of molecules. Imagine that each of these molecules will break down into XXX chemical compounds each acting on different parts of the body (cf. alcohol)? How can all these chemical effects and interactions be adequately studied from a physiochemical point of view? Is it enough to understand the end-results: i.e. people either feel better or worse without exactly knowing why?

I think that normal people take the decision based on only the end-results. But the experts may analyze the exact processes involved in breaking down a particular substance/chemical and its specific side effects on different body parts.

Allopathic thinking fosters the concept of "against." We must kill germs, kill viruses and kill bacteria. The reason these micro-organisms exist and our mutual relationship is ignored.

Read more : http://www.ehow.com/about_5655922_side-effects-allopathy.html

Allopathic medicines are wide spectrum having multiple effects. thus while one or a few of them may be favourable, others might be undesirable side effects.

One of the reason my be the chemical used are of artificial type..

Yes, may be because most of the chemicals used in allopathic medicines are artificial only.

Because, may be, artificial chemical are not suitable to all population sets and every circumstance.

Our stomach is a natural bio-reactor with host of bacterial beneficial to digest food and convert in to sugars of kind glucose, sucrose, etc 

When a allo-pathic medicine is consumed it is a particular chemical or combinations of chemicals which will react and may kill all the beneficial micro flora including the ones which it was suppose to kill

and cause some effect which are not expected

i also agree with above mentioned authors

May be because the ingredients used in preparation of all the medicines are mostly chemicals 

Yes, I fully agree with the views of @Prakash

Dear All,

Many of allopathic remedies are preparations of medicinal plants.  Their not complete efficiency can be explained that these medicinal plants have not been evolved to have been used as medical treatments. They have many sided and complex mechanisms of action. Their composition changes according to the environmental circumstances where they were collected or produced. Their efficiency is also various depending of the circumstances of use and the conditions of the treated persons. These substances effect very slowly. In summary, we do not know sufficiently these substances and their usage often is not suitably accomplished.

Dear Ajay,

Allopathic remedies are not exclusively artificial chemicals. Think on artemisinin (prepared of Artemisia  annua) a well-known drogue against malaria.  https://en.wikipedia.org/wiki/Artemisinin

Dear Ajay,

Allopathic remedies are not exclusively artificial chemicals. Think on artemisinin (prepared of Artemisia  annua) a well-known drogue against malaria.  https://en.wikipedia.org/wiki/Artemisinin

Dear Andras,

Yes, that's why I used the word 'most of the....' and not 'all'.

Dear Mario,

I agree with you on some aspects and I also have the similar concerns about RG.

Allopathy (or conventional medicine) is the most widespread system of medicines used worldwide at present. The simple reason is that it quickly gives relief from ailments in a patient. It is generally more favored than homeopathy or other alternate medicine systems. Allopathy makes use of drugs (which are mainly chemicals) that have an opposite effect to those of the symptoms. It works to suppress the symptoms of a disease in the minimum possible time. In some cases, the drugs cure the causes & not just the symptoms.

The most negative aspect of allopathy is the side effects since the drugs are mostly chemicals which treat, may react, and may decompose. A good MD has general awareness about these effects & may try to prescribe a proper combination of medicines to minimize them. A grave mistake occurs when a drug is exchanged between relatives or friends without consulting a MD.

Use of herbal supplements makes it important for dental surgeons, surgeons, and physicians to know about drug, food interaction, herbs and drugs interaction, and side effects of the herbal medications when taken together with allopathic medications, which can lead to serious complications if ignored.

http://www.civtedu.org/uploads/41572/ufiles/Webinar/Herbs_and_surgery_Natl_J_Maxillofac_Surg.pdf

Yes, Dear Krishnan,

When taken simultaneous, there are more chances of complications.

Ginger caused no side effects - The dosage used was equivalent to about one gram of the herb per day. The use of ginger herb daily beginning a few days before chemotherapy reduces nausea associated with the drug treatment.

http://www.raysahelian.com/chemotherapy.html

Agree with you dear @Brenda, that the inappropriate use of anything (even good) could be harmful.

May be one reasons:

Medicines test are dependent on environmental factor and  population.