This population-based study evaluates the prevalence of factitious disorders, Münchausen syndrome, and Münchausen syndrome by proxy in a clinical setting. All children referred to the Pediatric Unit of the Department of Pediatrics of the Catholic University Medical School (Agostino Gemelli Hospital) in Rome were recruited between November 2007 and March 2010. An experienced interdisciplinary team of medical professionals analyzed all suspected cases. A total of 751 patients were hospitalized. Factitious disorders were diagnosed in 14/751 patients, resulting in a prevalence of 1.8%. Three of 14 (21.4%) patients fulfilled the criteria for Münchausen syndrome. Münchausen syndrome by proxy was identified in four of 751 patients, resulting in a prevalence of 0.53%. The perpetrator was the mother in three of four of these cases. The epidemiological data obtained in this population-based study indicate that the prevalence of factitious disorders, Münchausen syndrome, and Münchausen syndrome by proxy is higher than previously observed. Moreover, early detection was possible thanks to the awareness of an expert interdisciplinary team. We suggest that physicians must consider the possibility of these diagnoses whenever there are discrepancies in a child’s illness presentation.