Hospitals are integrated with medical universities in Iran and are categorized into three types with respect to educational and health services quality. This cross-sectional study aimed to determine and compare the level of clinical competence of nurses who were working in type 1 and type 2 university hospitals. The clinical competence of all 266 nurses in the two hospitals was assessed by using the self-assessment method. The Nurse Competence Scale, a questionnaire consisting of 73 items, was used to assess the level of clinical competence and the frequency of using skills. The nurses who were working in the type 1 university hospital viewed themselves as more competent than those who were working in the type 2 university hospital. Also, only 70% of the clinical skills were used frequently by the nurses who were working in the type 2 university hospital, in comparison to > 83% for the nurses who were working in the type 1 university hospital. The results can be used for the educational needs assessment of nurses and for modifying the quality of care in hospitals.