ObjectiveTo investigate the clinical characteristics and prognosis of methicillinresistant Staphylococcus aureus (MRSA) infection in the special group and the normal group of children.MethodsBacterial isolation and identification were performed by routine methods, antimicrobial susceptibility testing was performed by KirbyBauer method. Sick children were grouped according to the source of children and Healthcareassociated Infection Diagnostic Criteria authorized by the Ministry of Health.ResultsSixtysix children with MRSA infection were admitted to the hospital in 2010, 30 of whom were the abandoned sick babies cured in Shanghai Municipal Welfare Home for Children(SMWHC). Communityassociated infection(CAI) group were neonates and contact infected children; infectionrelated factors in SMWHC group included severe malnutrition, surgical site infection, previous hospitalization, longterm bedridden/local compression; healthcareassociated infection (HAI) group was associated with chemotherapy after operation of malignant tumor, longterm nasal feeding, recent operation, tracheal intubation/mechanical ventilation. Average length of hospitalization was 40 days. The prognosis were as follows: All patients in CAI group were improved and discharged; 2 patients in SMWHC group died, mortality was 6.67%; 3 patients in HAI group died, mortality was 50%.ConclusionCharacteristics of MRSA infection in different groups varied significantly, the isolation treatment for the special children in the singleroom ward can reduce the cross infection between the CAMRSA and HAMRSA, as well as to reduce HAI.