For my experiments I go for male animals as I am interested in a disease which affects males. I think you just have to think what gender is most relevant to your question and then be consistent. Different hormones are at play in males and females so this is something to bare in mind and whether or not this is important for you. If you are testing a therapy which may be used in both males and females it may actually be interesting to see if the effect is the same in both genders... but then that requires sufficient numbers of each gender to be used.

For my experiments I go for male animals as I am interested in a disease which affects males. I think you just have to think what gender is most relevant to your question and then be consistent. Different hormones are at play in males and females so this is something to bare in mind and whether or not this is important for you. If you are testing a therapy which may be used in both males and females it may actually be interesting to see if the effect is the same in both genders... but then that requires sufficient numbers of each gender to be used.

In experiments being done in whole animals (in Vivo) if the gender is a confounding variable, we have to omit its effect and the best and simple way is to do this is to use only one gender in all groups of the study; male or female. Choosing male or female gender will be based on your protocol, disease and the indices you want to study. In female gender of laboratory animals usually it is too difficult to detect the exact phase of the menstrual cycle and naturally they will be in different phases of the cycle with different plasma levels of sex hormones. For this reason, usually we use male animals to have pure and accurate responses and then test it in female to see if the same results can be extended to female or not. However, if you are testing a therapy for a female-related disease, you need females. In most cases we test an unknown compound or on a unknown situation and have little information, it is wise to use male and when you have more information with more details, choose the most relevant gender.

In my experience, we nearly always use an equal number of males and females per study group and report the data by both sex and study group. This study design holds true for routine toxicology/carcinogenicity studies and also infectious disease studies (model characterization or therapeutic efficacy testing). The only exceptions have been sex-specific or reproductive diseases. It is true that there can be very different responses to the test article depending on sex, and there are also different incidences of background pathologic lesions, but I think that is critically important data.

For Invivo Animal Studies, using both the sex will be good to confirm the activity, except in few conditions. If the study is sex oriented like, gestational diabetes, aphrodisiac, uterine activity, etc. My suggestion is, when you are doing invivo which involves the toxic chemical to induce disease, prefer male, because they are genetically strong and blood volume is high than the female, so that the toxic concentration will be less in the plasma and less mortality rate.

Keep in mind that for a 2-year chronic rodent study, males may not be more robust than females due to aging conditions like nephropathy (rats) or liver neoplasia (mice).

Body structure, hormonal level and their nature vastly affect the outcomes of the experimental results in male and female animals. Choosing the gender greatly depends upon the type of experiments. For example estrogen hormone secreted by female animals is quite protective in several diseases including stroke. So female are not considered as the good models for stroke study. Similarly female are considered as good for multiple sclerosis study (EAE). Female got stress easily than male animals. So it depends upon the type of experiment and outcomes desire to chose the appropriate sex.

The paper Ali presented says it all.  Thank you Ali :o)

"Scientists have typically justified excluding female animals from experiments – even when studying conditions that are more likely to affect women – on the basis that fluctuating hormones would render the results uninterpretable. However, according to Rebecca Shansky, a neuroscientist at Northeastern University, in Boston, it is entirely unjustified by scientific evidence, which shows that, if anything, the hormones and behaviour of male rodents are less stable than those of females.

Shansky is calling for stricter requirements to include animals of both sexes in research, saying the failure to do so has led to the development of drugs that work less well in women." The Guardian, @hannahdev, Fri 31 May 2019 14.35 BST.

Article Are hormones a “female problem” for animal research?

The link for the paper mentioned. The only problem (specially with Ethics Committees) is that we might use more animals.