There are few data about the epidemiology of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) among children in Israel. This study was intended to identify risk factors for CA-MRSA colonization in healthy infants, to characterize the molecular features of colonizing organisms, and to determine whether they are responsible for health care-associated (HA) infections. Nasal cultures and demographic details were collected from a cohort of healthy infants at 5 visits between the ages of 2 and 12 months. Clinical characteristics of pediatric MRSA bloodstream infections (2001 to 2006) and wound cultures collected over 6 months were also studied. Clonal structure was evaluated by multilocus sequence typing. Isolates were studied for the staphylococcal cassette chromosome mec (SCCmec) type and for the presence of Panton-Valentine leukocidin (PVL) genes. MRSA was cultured at least once from 45 of 659 infants (346 Jewish and 313 Bedouin infants). Forty of 45 (89%) isolates were from Bedouin infants. Twenty-nine of 45 (64.4%) belonged to a new clonal complex, designated CC913, that carries SCCmec IV but not the PVL genes. CC913 was also isolated from 9/14 blood cultures and 7/8 wounds. All CC913 infections occurred in Bedouin children, and all but two were HA. In conclusion, Bedouin origin was the main risk factor for carriage of CA-MRSA. CC913 was dominant both in healthy carriers and as a cause of pediatric HA-MRSA bloodstream infections.