BACKGROUND: There is an intimate association between chronic pain and substance use disorders, and it is difficult to manage these conditions without causing significant morbidity. Many studies have shown that exercise can alleviate chronic pain. The purpose of this study was to evaluate the impact of yoga and Pilates on pain and mood scores among those with chronic pain at a womens' substance use treatment facility. METHODS: This is a prospective questionnaire-based pilot study. One hour of Vinyasa Yoga and 1 h of mat Pilates classes were offered weekly at a women's substance use treatment center between November 11, 2016 and December 16, 2017. Questionnaire data was collected to assess the role of these modalities on pain and mood scores. Descriptive statistics, chi square for categorical outcomes and t-test for continuous outcomes were used for analysis. RESULTS: Among the women in residential rehabilitation for substance use disorder, 37% had chronic pain and the odds ratio of having a prior relapse within this group was 2.8 (95% CI: 1.5-5.4). These classes primarily heightened mood, decreased anxiety, improved self-image and only 21.7% of respondents noted improved pain management. Participants reported an average pain decrease of 0.19 and mood improvement of 0.11 units per week on a scale of 0-10. While pain control was not the primary benefit or motivation behind the classes, pain scores consistently decreased over the course of the study. CONCLUSION: Pain scores improved synergistically with enhanced mood as part of this yoga and Pilates intervention. Yoga and stretching were cited as more beneficial then strengthening, meditation and Pilates. Further studies should be conducted to illuminate whether these interventions could prevent relapse in this population.