Objective: In the much complex and dynamic system of health, the smallest difference in services leads to increase in customer demand. Medical centers and hospitals need to expand internet and Application Service Providing (ASP) and to convert that in to a competitive, long-lasting choice. The present study was carried out with the aim of determining the relationship between the quality of service providing software systems and customer satisfaction in selected hospitals of Tehran University of Medical Sciences using similar hospital information systems. Methodology: This research is a correlation, descriptive analysis. The statistical group includes employees in the hospital revenue and clearance unit and the study was carried out through census and using questionnaire. To analyze the data, SPSS software was used and in addition to descriptive statistics of: tables, frequency distribution percentage and average, inferential statistics like KS and Pearson tests were used. Results: With a 95% confidence level one can conclude from this study that there is a meaningful relationship between the quality of service providing software programs with customer satisfaction in the selected hospitals of Tehran University of Medical Sciences. Also, the results showed that the intensity of the relationship between satisfaction and other variables of system quality, service quality and information quality is 0.734, 0.721 and 0.521 respectively (P<.05). Conclusion: Although all variables have positive and meaningful relationship with customer satisfaction, their average is less than moderate limit so the managers in the field of health are advised to consider these issues in their management methods.