In case of extraction its ethanol which is better and safe. In case of fractionation, isolation and further studies non-chlorinated solvents should be used.
Methanol does not absorb moisture like ethanol, if your sample is not for administration to a biological system methanol does its job better than ethanol. Preliminary phytochemical testing, TLC, CC etc i prefer MeOH. If for any activity screening in a living system go for EtOH.
For safety reason I recomment EtOH. I still remembered one natural product chemist saying that MeOH would make his eye uncomfortable and he uses EtOH as long as MeOH is not a must.
Methanol is the best solvent system to extract phytochemicals. Because methanol has high extractability in compare with Ethanol. methanol and its polarity work on vast number of phytochemicals including Polar and non polar compounds. the extractability we can assure atleast 50% on both side of the polarity. This may be due to non azeotrope nature of methanol.
as other experts said, biological assays Ethanol extraction is preferred.
It all depends on what you want to study. For very preliminary studies 50% hydroalcoholic extraction will be better. Methanol can also do the same work. However, it is poisonous. Ethanol is safe.
I would suggest methanol for phytochemical analysis due to wide range of compounds with different polarity (non-polar to polar) that could be extracted from a plant sample with this solvent. If a total extraction with maceration technique will be performed, then methanol is preferred than ethanol. On the other hand, if further research is for animal studies, then starting with less toxic ethanol (absolute) or aqueous ethanol should be considered.
Following factors should be considered when selecting a solvent for commercial extraction plant utilization:
solvent power (selectivity);
combability with local legislation about permitted solvent levels in the product - this is particularly important for food applications.
boiling temperature - this should be low in order to facilitate removal of the solvent from the product;
latent heat of vaporization;
reactivity - the solvent should not react chemically with the extract, nor should it readily decompose;
viscosity - must be low;
stability to heat, oxygen and light;
safety in use - the solvent should, if possible, be non-flammable and should not present a toxicity hazard to technicians or consumers; its disposal should not endanger the environment;
the solvent should be available in substantial quantities;
cost;
suitability for re-use;
rom my experiences in extractions methanol is the best alcoholic solvent for most phytochemical compounds and when calculating their quantities they are highest in methanolic extract comparing to the ethanolic. Safety should not be neglected, some traces of methanol remains with extract and in long term uses are not safe. The following factors should be considered when selecting a solvent for commercial extraction plant utilization:
it depends on the situation at hand if the extraction requires the use of a biological system then Ethanol should be prefered. but if it does not involve a biological system Methanol will do better.