Introduction Human laboratory paradigms for examining stress- or cue-reactivity in substance-dependent individuals often involve exposure to pharmacological, psychosocial or physical laboratory procedures or drug paraphernalia. This study examines whether participation in such studies alters drug-seeking behavior and which patient attributes contribute to increased use. Methods In two separate studies, the relationship between participation and drug use post-study were examined. Cocaine-dependent participants received 1 μg/kg of corticotropin releasing hormone intravenously, underwent the Trier Social Stress Task, and were exposed to drug cues and various measures obtained. Cocaine use for 90 days prior and 28 days following the study was assessed. Methamphetamine-dependent participants were exposed to drug cues and various measures obtained. Methamphetamine use for 90 days prior and 14 days following the study was assessed. Weekly drug use was modeled using a 2-state hidden Markov model assuming two possible underlying states at each week. Bayesian estimation was used. Results are presented as posterior mean odds ratios (OR) and 95% credible intervals (CI). Results Participation decreased the odds of remaining in or transitioning to the high use state (cocaine study OR = 0.04 [CI = 0.01, 0.11]; methamphetamine study OR = 0.39 [CI = 0.07, 1.70]). In the cocaine study, older age increased the odds of remaining in or transitioning into the high use state (1.66 [CI = 0.99, 2.96]). In the methamphetamine study, male gender increased the odds (2.70 [CI = 1.10, 6.17]). Conclusion Stress and cue exposure paradigms were associated with a decreased odds of drug use following participation.