We report on a study of 35 methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates collected between February and May 1998 from 4 different hospitals in Northern and Southern Palestine. The isolates were recovered from infection and carriage sites of patients and hospital environmental samples. The arbitrarily primed PCR (AP-PCR) method with two primers appears to be a useful tool, provides a fast and simple method for genetic analysis of MRSA infections and allows us to differentiate 22 different AP-PCR patterns. The major cluster, however, sharing common AP-PCR as well as a common PFGE pattern, represented 34% of all MRSA isolates. Isolates of this cluster were spread throughout the neonatal and intensive care units of Rafidya hospital during the entire period. In addition, these isolates were distributed in the southern part of Palestine as well.