Strategies to control and prevent the spread of methicillin-resistant Staphylococcus aureus (MRSA) include early identification of positive patients through screening, patient isolation, hand hygiene, nasal and skin decontamination, and the adequate cleaning and decontamination of clinical areas. However, many national and other guidelines provide few details on environmental decontamination regimens, partly because the role of the environment in the spread of MRSA is not well documented. We prospectively studied the environment of the isolation rooms of 25 MRSA patients for up to four weeks, sampling horizontal surfaces and the air using settle plates as well as an air sampler, while continuing regular daily cleaning according to the hospital protocol. We then typed 20 patient isolates and the corresponding environmental isolates (N=35) to assess the similarity of strains. A high proportion of samples were positive for MRSA; 269/502 (53.6%) surface samples, 70/250 (28%) air samples and 102/251 (40.6%) settle plates. Over half of the surface samples taken from the beds and the mattresses were positive for MRSA. Identical or closely related isolates were recovered from the patient and their environment in 14 (70%) patients, suggesting possible environmental contamination of the isolation rooms, possibly contributing to endemic MRSA. More effective and rigorous use of current approaches to cleaning and decontamination is required as well as consideration of newer technologies to eradicate MRSA and other hospital-acquired pathogens.