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Providing collaborative mental health treatment within primary care settings improves depression outcomes and may improve detection of mental disorders. Few studies have assessed the effect of collaborative mental health treatment programs on diagnosis of mental disorders in primary care populations. In 2008, many Department of Veterans Affairs (VA) facilities implemented collaborative care programs, as part of the VA's Primary Care–Mental Health Integration (PC-MHI) program.To assess the prevalence of diagnosed mental health conditions among primary care patient populations in association with PC-MHI programs, overall and for patient subpopulations that may be less likely to receive mental health treatment.Using a difference-in-differences analysis, we evaluated whether the rates of psychiatric diagnoses among primary care patient populations at 294 VA facilities changed from fiscal year (FY)07 to FY08, and whether trends differed at facilities with PC-MHI encounters in FY08. Subgroup analyses examined whether trends differed by patient age and race/ethnicity.From FY07 to FY08, the prevalence of diagnosed depression, anxiety, post-traumatic stress disorder, and alcohol abuse increased more in the 137 facilities with PC-MHI program encounters than in the 157 facilities without these encounters. Increases were more likely among patients who were younger (18–64) and white.Initiation of PC-MHI programs was associated with elevated diagnosis patterns, which may enhance recognition of mental health needs among primary care patients. Increases in diagnosis prevalence were not uniform across patient subgroups. Further research is needed on treatment processes and outcomes for individuals receiving services in PC-MHI programs.