BackgroundMeasuring patients’ perception from health service quality as an important element in the assessment of service quality has attracted much attention in recent years. Therefore, this study was conducted to find out how the patients evaluated service quality of clinics at teaching hospitals affiliated with Tehran University of Medical Sciences in Iran.MethodsThis cross-sectional study was conducted in Tehran in 2017 and 400 patients were randomly selected from four hospitals. Data were collected using a questionnaire, the validity and reliability of which were confirmed in previous study. In order to analyze the data, T-test, ANOVA, and Pearson correlation coefficient were calculated using SPSS 23.ResultsThe results indicated that among eight dimensions of health service quality, the patients were more satisfied with physician consultation, services costs and admission process. The highest and lowest mean scores were related to physician consultation (Mean = 4.17), and waiting time (Mean = 2.64), in that order. The total mean score of service quality was 3.73 (± 0.51) out of 5. Outpatient services were assessed as good, moderate and weak by 57.5, 40 and 2.5% of the patients, respectively. There was a significant relationship between the positive perception of service quality and reason for admission, source of recommendation, gender, education level, health status, and waiting time in the clinics (p <  0.05).ConclusionThe majority of the patients had a positive experience with visiting clinics and perceived service provision as good. In fact, patients’ perceptions of physician consultation, provision of information to patients and the environment of delivering services, are the most important determinants of service quality in clinics.