Accurately measuring and accounting for confounds frequently present in adolescent substance-using populations is essential for elucidating the true effect of substance use on adolescent neurocognitive functioning. Common confounds in this population include head injury, depression, ADHD, conduct disorder, prenatal exposure to neurotoxins, family history-related effects, and polysubstance involvement. Conversely, excluding subjects for the aforementioned confounds may impede the generalizability of results. The tradeoff between minimizing confounds and having meaningful, ecologically valid results is an important study design decision, especially given the high cost of fMRI sessions.