Background: Chronic diseases, particularly cardiovascular diseases and diabetes, continue to lead the way with regard to mortality as well as morbidity in the United States. Despite several efforts to prevent the onset of these diseases in the last couple of decades, the burden of chronic diseases continues to rise. The burden of chronic diseases has increased more rapidly among disparate populations, particularly among ethnic minorities, rural, and those in the lower socio-economic status. Rationale for Study: In an effort to reach the disparate populations, health disparities collaborative was implemented in Louisiana in 2010 in three federally qualified health centers to improve delivery of quality care and improve health outcomes for patients diagnosed with diabetes and heart disease. Materials and Methods: A qualitative study was conducted using individual face-to-face interviews at each clinical site to assess the level of implementation, satisfaction with the initiative, and challenges and barriers in implementing the initiative. Data in this qualitative study were analyzed using interpretative coding. Results: All three clinical sites expressed satisfaction in implementing the collaborative and appreciated the coordinated efforts to treat chronic diseases among their patients. Interpretation: Although the implementation of chronic disease collaborative appeared to be very successful based on the qualitative data as well as clinical outcomes, several challenges in implementation were observed. Results of the study indicated a need for strong leadership at the clinical sites, enhanced communication efforts to engage the collaborative team, and increased emphasis on patient education for successful implementation of the collaborative.