Introduction The presented research sought to understand variation in the clinical quality of general practice. Methods Clinical quality indicators relating to Cardiovascular Disease and Diabetes were analysed in general practices in Sandwell and the Black Country. General practices showing unusually high or low performance across indicators were identified. Semi-structured interviews were then conducted with practice staff to explore reasons for variation. Results Differences emerged between practices' leadership, culture, care systems and approaches to quality measurement and improvement. General practices were categorised into four types within a newly developed typology of general practice organisations: "biomedical", "holistic", "corporate" and "externally reactive", where there was some evidence that practice type influenced variation. Discussion Variation in general practice clinical quality appeared linked to differences staff held in their views of what constitutes quality in general practice, as explained through the practice typology, with an implied trade-off between achievement of different quality priorities. The research is limited by the study population, specified disease focus and quality measures adopted to examine variation. However, the results highlight the importance of moving to a shared definition of quality in general practice which may influence the measurement and understanding of variation in this setting and the developed practice typology.