Growing evidence points to the role of epigenetic mechanisms, including DNA methylation, in substance use and addiction. We conducted a systematic review of 47 recent (2012-15) animal and human studies that investigate DNA methylation and substance use/exposure, spanning preconception to adulthood. The majority of extant studies (i) focused on exposure during adulthood, (ii) examined the effects of alcohol use, (iii) employed a candidate gene approach and (iv) were cross-sectional. While studies generally support an association between substance use/exposure and DNA methylation, and also suggest that developmental context and timing matter, dearth of longitudinal data and low comparability across studies currently limits the conclusions that can be drawn. Future challenges and directions for the field are discussed.