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Background: The aim of this study was to compare the changes in primary (heroin use-related) and secondary (depressive symptoms and quality of life, QOL) outcome indicators of 3-month methadone maintenance treatment (MMT) between heroin users with and without HIV infection. Methods: A total of 242 intravenous heroin-dependent individuals (30 with and 212 without HIV infection) receiving MMT were recruited. Primary (severity of heroin dependence, harm caused by heroin use and current heroin use) and secondary (depressive symptoms and QOL) outcome indicators were determined before and after receiving 3-month MMT. Changes in primary and secondary outcome indicators between the two groups were compared using mixed-model analysis. Results: Heroin users both with and without HIV infection showed significant improvement in three primary outcome indicators after 3-month MMT, and there was no difference in the changes of these primary outcome indicators between the two groups. However, improvements in depressive symptoms and the physical domain of QOL among HIV-infected heroin users were poorer than in those without HIV infection. Conclusions: The results of this study indicated that heroin users with HIV infection did improve in the primary but not the secondary outcomes after 3-month MMT. [ABSTRACT FROM AUTHOR]