Background: We evaluated a facilitation strategy to help clinical sites likely to experience challenges implement evidence-based Primary Care-Mental Health Integration (PC-MHI) care models within the context of a Department of Veterans Affairs (VA) initiative. This article describes our assessment of whether implementation facilitation (IF) can foster development of high quality PC-MHI programs that adhere to evidence, are sustainable and likely to improve clinical practices and outcomes. Methods: Utilizing a matched pair design, we conducted a qualitative descriptive evaluation of the IF strategy in sixteen VA primary care clinics. To assess program quality and adherence to evidence, we conducted one-hour structured telephone interviews, at two time points, with clinicians and leaders who knew the most about the clinics' programs. We then created structured summaries of the interviews that VA national PC-MHI experts utilized to rate the programs on four dimensions (overall quality, adherence to evidence, sustainability and level of improvement). Results: At first assessment, seven of eight IF sites and four of eight comparison sites had implemented a PC-MHI program. Our qualitative assessment suggested that experts rated IF sites' programs higher than comparison sites' programs with one exception. At final assessment, all eight IF but only five comparison sites had implemented a PC-MHI program. Again, experts rated IF sites' programs higher than their matched comparison sites with one exception. Over time, all ratings improved in five of seven IF sites and two of three comparison sites. Conclusions: Implementing complex evidence-based programs, particularly in settings that lack infrastructure, resources and support for such efforts, is challenging. Findings suggest that a blend of external expert and internal regional facilitation strategies that implementation scientists have developed and tested can improve PC-MHI program uptake, quality and adherence to evidence in primary care clinics with these challenges. However, not all sites showed these improvements. To be successful, facilitators likely need at least a moderate level of leaders' support, including provision of basic resources. Additionally, we found that IF and strength of leadership structure may have a synergistic effect on ability to implement higher quality and evidence-based programs.