Lepidium meyenii, known as maca, is a popular nutraceutical food which is grown over 4,000 m above sea level in the Peruvian central highlands. Maca contains alkaloids, but there are no studies on their biological effects. The butanol fraction obtained from methanol extract of maca hypocotyls contains alkaloids. The effects of butanol/aqueous fractions partitioned from methanol extract of yellow and black maca were examined. Total phenolic content (TPC) and antioxidant capacity by 2,2'-diphenyl-1-picrylhydrazyl were used to evaluate maca fractions in vitro. Daily sperm production and sperm count in epididymis and vas deferens in mice were determined as biological effect of maca extracts in vivo. Yellow maca (21.7%+/-0.69) had better antioxidant capacity than black maca (18.2% +/- 0.12; p < .01). Antioxidant activity was better in the methanolic fraction than in the aqueous fraction of yellow or black maca. TPC is higher in the aqueous fraction than in the methanolic extract of yellow or black maca. Black maca administration resulted in higher concentration of sperm count in epididymis and vas deferens compared to yellow maca. A higher biological effect was observed in methanolic extract and in aqueous extract than in the butanol fraction of maca. In conclusion, better biological effect was observed in the methanolic extract of maca than in its partitioned fractions.