Background Multisite qualitative studies are challenging in part because decisions regarding within-site and between-site sampling must be made to reduce the complexity of data collection, but these decisions may have serious implications for analyses. There is not yet consensus on how to account for within-site and between-site variations in qualitative perceptions of the organizational context of interventions. The purpose of this study was to analyze variation in perceptions among key informants in order to demonstrate the importance of broad sampling for identifying both within-site and between-site implementation themes. Methods Case studies of four sites were compared to identify differences in how Department of Veterans Affairs (VA) medical centers implemented a Primary Care/Mental Health Integration (PC/MHI) intervention. Qualitative analyses focused on between-profession variation in reported referral and implementation processes within and between sites. Results Key informants identified co-location, the consultation-liaison service, space, access, and referral processes as important topics. Within-site themes revealed the importance of coordination, communication, and collaboration for implementing PC/MHI. The between-site theme indicated that the preexisting structure of mental healthcare influenced how PC/MHI was implemented at each site and that collaboration among both leaders and providers was critical to overcoming structural barriers. Conclusions Within- and between-site variation in perceptions among key informants within different professions revealed barriers and facilitators to the implementation not available from a single source. Examples provide insight into implementation barriers for PC/MHI. Multisite implementation studies may benefit from intentionally eliciting and analyzing variation within and between sites. Suggestions for implementation research design are presented.
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