Introduction. Recognizing factors affecting job motivation can be very helpful in increasing efficiency and job satisfaction of university faculty members. In order to Identify the internal and external factors of job motivation, this study was conducted to determine the effective factors on job motivation of faculty members in Rafsanjan Medical University. Methods. In a descriptive study, all faculty members of Rafsanjan Medical University (n=82) completed a questionnaire developed by the investigator based on Herzberg’s theory and consisted of 40 questions. The validity and reliability of the questionnaire was confirmed by content validity and test re-test. The data was analyzed by SPSS software using frequency distribution and chi2.Results. Eighty one percent of faculty members considered external factors and 72% considered internal factors important in job motivation. Among the external factors, wage and sallary, job security, work environment, communication with others, supervision and the work policy had the most important role, respectively. The most important internal factors included nature of the job, appreciation of employees, professional development and job success, respectively.Conclusion. Based on the faculty members’ view points, the external factors (hygiene factors) compared with the internal factors (motivation factors) had a more important role in job motivation which does not conform with the Herzberg’s view. Salary and job security were the most important motivation factors.