This study investigates the effects of work context on professional job processes in large organizations in general, and the differences of perceptions and expectations of physicians for professional autonomy in different work environments in specific. An empirical study was conducted on "perceptions and expectations of physicians" in terms of their control over diagnosis and treatment process in different teaching hospitals in Turkey. Results exhibit that the difference between expectation and perception on "the control over diagnosis and treatment process", one of the crucial elements in professional autonomy of physicians, is statistically significant among the surveyed hospitals. The reason of this difference seems to be the managerial practices of each organization. Thus, the study emphasizes the need of assessing the problematic job procedures and of changing them with the most effective ones to create a synergy instead of conflict in the work setting. This synergy in the health care organizations means a balance between managerial control and professional autonomy and a better health service to the patient.