The performance of general practitioners (GPs) is frequently assessed without considering the factors causing variability among general medical practices (GMPs). Our cross-sectional national-based study was performed in Hungary to evaluate the influence of GMP characteristics on performance indicators. The relationship between patient's characteristics (age, gender, education) and GMP-specific parameters (practice size, vacancy of GP's position, settlement type, and county of GMP) and the quality of care was assessed by multilevel logistic regression models. The variations attributable to physicians were small (from 0.77% to 17.95%). The education of patients was associated with 10 performance indicators. Practicing in an urban settlement mostly increased the quality of care for hypertension and diabetes care related performance indicators, while the county was identified as one of the major determinants of variability among GPs' performance. Only a few indicators were affected by the vacancy and practice size. Thus, the observed variability in performance between GPs partially arose from demographic characteristics and education of patients, settlement type, and regional location of GMPs. Considering the real effect of these factors in evaluation would reflect better the personal performance of GPs.