BACKGROUND: Pain in opioid-dependent patients is common but data measuring the course of pain (and its correlates) using validated scales in patients initiating methadone treatment are sparse. We aimed to assess pain and its interference in daily life, associated correlates, and undertreatment before and during methadone treatment. METHODS: This is a secondary analysis using longitudinal data of a randomized trial comparing two methadone initiation models. We assessed the effect of methadone initiation and other correlates on pain intensity and interference (using the Brief Pain Inventory) at months 0, 6 and 12 using a mixed multinomial logistic regression model. RESULTS: The study group comprised 168 patients who had data for either pain intensity or interference for at least one visit. Moderate to severe pain was reported in 12.9% of patients at M0, 5.4% at M6 and 7.3% at M12. Substantial interference with daily functioning was reported in 36.0% at M0, 14.5% at M6 and 17.1% at M12. Of the 98 visits where patients reported moderate to severe pain or substantial interference, 55.1% reported no treatment for pain relief, non-opioid analgesics were reported by 34.7%, opioid analgesics by 3.1% and both opioid and non-opioid analgesics by 7.1%. Methadone was associated with decreased pain intensity at 6 months (OR = 0.29, p = 0.04) and 12 months (OR = 0.30, p = 0.05) of follow-up and tended to be associated with substantial pain interference. Suicide risk was associated with both pain intensity and pain interference. CONCLUSIONS: Methadone in opioid-dependent patients can reduce pain. However, undertreatment of pain in methadone patients remains a major clinical concern. Patients with pain are at higher risk of suicide. Adequate screening and management of pain in this population is a priority and needs to be integrated into routine comprehensive care.