Homocysteine is an amino acid produced in the liver that, when present in high concentrations, is thought to contribute to plaque formation and, consequently, increased risk of cardiovascular disease. However, daily physical activity and training programs may contribute to controlling atherosclerosis. Given that physical exercise induces changes in protein and amino acid metabolism, it is important to understand whether homocysteine levels are also affected by exercise and to determine possible underlying mechanisms. Moreover, regarding the possible characteristics of different training programs (intensity, duration, repetition, volume), it becomes prudent to determine which types of exercise reduce homocysteine levels. To these ends, a systematic review was conducted to examine the effects of daily physical activity and different training programs on homocysteine levels. EndNote was used to locate articles on the PubMed database from 2002 to 2013 with the keyword combinations ‘‘physical activity and homocysteine’’, ‘‘training and homocysteine’’, and/or ‘‘exercise and homocysteine’’. After 34 studies were identified, correlative and comparative studies of homocysteine levels revealed lower levels in patients engaged in greater quantities of daily physical activity. Regarding the acute effects of exercise, all studies reported increased homocysteine levels. Concerning intervention studies with training programs, aerobic training programs used different methods and analyses that complicate making any conclusion, though resistance training programs induced decreased homocysteine levels. In conclusion, this review suggests that greater daily physical activity is associated with lower homocysteine levels and that exercise programs could positively affect homocysteine control.