Despite the commonness of scabies in Japanese institutional settings, the nationwide prevalence of scabies has not been elucidated. This study was conducted to assess the prevalence of scabies and control measures in Japanese hospitals. A questionnaire on scabies epidemiology (e.g. number of patients and onsets of outbreak) and preventive measures were sent to psychiatric hospitals and long-term care hospitals nationwide (n = 1795) in January 2005. Seven hundred and forty-one hospitals responded (41.3%). Three hundred and thirty-three (44.9%) respondent hospitals had one or more scabies cases in 2004. Among 159 hospitals that had experienced scabies outbreak, only 32 of them reported cases of crusted scabies. Multivariate regression analysis showed that hospitals had a greater number of beds, and that acute- and long-term care wards were more likely to experience scabies onsets. Hospitals that compiled their infection control manuals on scabies, treated suspicious patients with scabicides without confirmed diagnosis, and performed skin checkup of inpatients were more likely to experience scabies cases. Infection control personnel should be aware that unrecognized crusted scabies can cause outbreaks. Higher patient turnover is a risk factor for scabies introduction into a hospital. Preventive measures against scabies, such as patient screening at admission and treating all suspicious patients without confirmed diagnosis, were not effective to avoid scabies introduction.