Long-term care facilities are vulnerable to outbreaks of influenza. This report describes the response to such an outbreak in a long-term care facility for severely handicapped children and adults near Ljubljana, Slovenia, in March and April 2009. Of the 23 residents who lived in a unit of the facility, 10 fell ill with fever (>or=37.5 degrees C) during a period of nine days. Probable and confirmed cases were residents who developed a fever after 24 March 2009. Respiratory symptoms were not included in the case definitions as some residents were unable to describe their symptoms due to their mental and/or physical impairment. Epidemiological data were collected and throat and nasal swabs taken. Influenza A virus was identified (without subtyping) and treatment with oseltamivir was given to patients with fever of no more than 48 hours' duration. Oseltamivir was also given prophylactically to healthy residents and staff. Rigorous adherence to standard and droplet precautions was recommended by the regional institute of public health. Two days after respiratory and standard precautions have been strengthened, four more residents became ill. Viral subtyping showed that 12 of the 23 residents were infected with influenza virus A(H1N1); one had an influenza B virus infection. Of the 12 confirmed influenza A cases, 10 had been vaccinated with the seasonal influenza vaccine. Follow-up swabs were taken and were found to be still positive for influenza A virus in 6 of the 12 confirmed cases more then a week after illness onset. The virus was resistant to oseltamivir and susceptible to zanamivir. This influenza outbreak demonstrates the need for rapid typing and subtyping of influenza viruses for accurate diagnosis, treatment and chemoprophylaxis in special settings.