Introduction: Various types of software are used in health care organizations to manage information and care processes. The quality of software has been an important concern for both health authorities and designers of Health Information Technology. Thus, assessing the effect of software quality on the performance quality of healthcare institutions is essential.Method: The most important health care quality indicators in relation to software quality characteristics are provided via an already performed literature review. ISO 9126 standard model is used for definition and integration of various characteristics of software quality. The effects of software quality characteristics and sub-characteristics on the healthcare indicators are evaluated through expert opinion analyses. A questionnaire comprising of 126 questions of 10-point Likert scale was used to gather opinions of experts in the field of Medical/Health Informatics. The data was analyzed using Structural Equation Modeling.Results: Our findings showed that software Maintainability was rated as the most effective factor on user satisfaction (R2=0.89) and Functionality as the most important and independent variable affecting patient care quality (R2=0.98). Efficiency was considered as the most effective factor on workflow (R2=0.97), and Maintainability as the most important factor that affects healthcare communication (R2=0.95). Usability and Efficiency were rated as the most effectual factor affecting patient satisfaction (R2=0.80, 0.81). Reliability, Maintainability, and Efficiency were considered as the main factors affecting care costs (R2=0.87, 0.74, 0.87).Conclusion: We presented a new model based on ISO standards. The model demonstrates and weighs the relations between software quality characteristics and healthcare quality indicators. The clear relationships between variables and the type of the metrics and measurement methods used in the model make it a reliable method to assess the effect of software quality on healthcare organizations’ quality performance.