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Introduction: In fact, management of information technology in the health system, designing the hospital information systems and electronic medical records in the health care centers, need to train some specialists familiar with computer science and Information Technology as well clinical knowledge and health systems. This study aimed to compare training programs and professional needs from the viewpoint of health information technology graduates. Method: This is a descriptive-analytic and cross-sectional survey on the 120 Bachelor graduated in Health Information Technology of Zahedan School of Allied Medical Sciences in 2016. Data were collected by using a standard questionnaire with confirmed validity and reliability and analyzed using SPSS 16. Results: The results show that most of first-year students (% 75) had good ability in using Information Technology in their job. More first-year students believed that training courses (% 48/9) compared to the theoretical (% 41/6) and practical (% 35/5) courses were more effective and applicable in professional performance. On the other hand, most graduates declared that lack of technical skills (% 38/7) is the main factor causing psychological pressure in the first-year students although the level of this pressure in the second- year students and in third-year students were medium and low, respectively. Conclusion: Considering the results, relationship between the goals of training programs and professional needs in the field of health information technology was declining. Therefore, there are urgent need to change training courses in order to improve the professional skills of graduates and meet their professional needs.