Based on evidence from the existing substance dependence literature, we identified a hierarchical factor model that provided good fit to alcohol, marijuana, and cocaine dependence symptom data in both a community-sampled and a clinically over-selected study. Measurement invariance of the model across samples and between sexes demonstrates that patterns of differences in criterion endorsement rates between these groups are primarily explained by mean differences in a higher-order multi-substance dependence trait, rather than being specific to individual substances or symptom parameters. Our findings support the psychometric validity of combining population and clinical samples in explorations of substance dependence etiology and outcomes.