OBJECTIVE: Determine, using fuzzy set qualitative comparative analysis (fs/QCA), the relationship between patient-centered medical home (PCMH) systems and quality in 21 NCQA recognized medical homes. DATA SOURCES/STUDY SETTING: Primary data collected in 2009, including measures of optimal diabetes care (ODC), preventive services up-to-date (PSUTD), patient experience (PEX), survey data assessing PCMH capabilities (PPC-RS), and other clinic characteristics. STUDY DESIGN: Cross-sectional study identifying associations between PPC-RS domains, demographic, socioeconomic, and co-morbidity measures, and quality outcomes. DATA COLLECTION/EXTRACTION METHODS: PPC-RS scores were obtained by surveying clinic leaders. PSUTD and ODC scores were obtained from provider performance data. PEX data were obtained from patient surveys. Demographic, socioeconomic, and co-morbidity data were obtained from EMR and census data. PRINCIPAL FINDINGS: fs/QCA identified associations between all three outcomes and PCMH capabilities: ODC and team-based care; PSUTD and preventive services systems; and all three outcomes and provider performance reporting systems. Previous statistical analysis of this data had failed to identify these relationships. CONCLUSIONS: fs/QCA identified important associations that were overlooked using conventional statistics in a small-N health services data set. PCMH capabilities are associated with quality outcomes.