Physical pain among persons seeking treatment for substance use disorders (SUD) and characteristics associated with pain were examined in a secondary analysis of data from the Drug Abuse Treatment Outcome Study (DATOS), a multi-site treatment outcome study. Patients (N = 7,876) in four treatment modalities—long-term residential (LTR), short-term inpatient (STI), outpatient methadone treatment (OMT), and outpatient drug-free (ODF)—reported severity of physical pain experienced during the preceding 12 months. Moderate to severe physical pain was reported by 21.2% of LTR patients, 26.8% of STI patients, 33.6% of OMT patients, and 17.6% of ODF patients. Individuals with and without physical pain were compared across treatment modalities. Patients with pain were more likely to report weekly heroin use [aOR = 1.73 (1.44–2.08)], weekly narcotics use [aOR = 1.43 (1.18–1.74)] and greater depressive symptoms [aOR = 1.30 (1.21–1.38)]. These findings support the presence of a sizable proportion of SUD patients with pain who may benefit from pain assessment as part of their SUD treatment.