Introduction: Clinical competence of nurses working in the neonatal intensive care units together with advancements in medical science and technology increased the survival rate of newborns that need specialized care. To ensure the quality of care and provide the safety of patients, evaluating the clinical competence of nurses seems necessary. This study aimed to evaluate the clinical competence of nurses in the neonatal intensive care units. Methods: In this cross-sectional study, 117 nurses working in the neonatal intensive care units of the hospitals affiliated to Tehran University of Medical Sciences were selected by census method. The research tool was Development of Competency Inventory for Registered Nurses questionnaire which completed by self-assessment. The mean clinical competence scores of participants categorized into 3 levels: weak: <225, moderate: 225-273 and good: >273. Data were analyzed by SPSS version 13 using the Pearson correlation coefficient, t-test and Chi-square test. Results: The highest levels of competence were related to critical thinking and research attitude and interpersonal relationships, and the lowest level was related to training and mentoring. There was a direct statistically significant relationship between marital status, employment status, level of interest in working in the neonatal intensive-care units and the clinical competence of nurses. Conclusion: Since the clinical competence of nurses in the Neonatal Intensive Care Units is vital, some variables such as interest in the nursing profession, employment status, the neonatal intensive theoretical and practical training courses and the amount of overtime working hours should be taken into consideration.