Objective To investigate the risk factors for nosocomial infections in rehabilitation department of a general hospital. Methods The infection rate, underlying diseases and infection sites were retrospectively reviewed in 1243 patients hospitalized in rehabilitation department of the Second Affiliated Hospital of Wenzhou Medical College from July 1, 2004 to June 30, 2008. Risk factors were determined by multivariate analysis with Logistic regression. Results The infection rate and the frequency of nosocomial infections in rehabilitation department were 18. 34 % (228/1234) and 21. 40 % (266/1243), respectively. Patients with spinal cord injury and those with cerebrovascular diseases accounted for 41.67% (95/228) and 31. 14% (71/228) of the total nosocomial infections, respectively. Urinary tract and lower respiratory tract were the frequent infection sites. The incidence of nosocomial infections was correlated with underlying diseases, age, length of stay, invasive operation, nutrition, sensory or movement disturbance and dysphagia. Conclusions Rehabilitation department has high nosocomial infection rate. Relevant risk factors should be carefully monitored to prevent or reduce the occurrence of the infections.