We surveyed members of the Society for Healthcare Epidemiology of America to assess current practice with regard to identifying and eradicating methicillin-resistant Staphylococcus aureus (MRSA) colonization in the neonatal intensive care unit (NICU). Although most respondents (86%) screened patients for MRSA colonization, variation existed in the number of anatomic sites sampled and in the use of culture at NICU admission, empirical institution of isolation precautions, and MRSA decolonization therapy. Evidence-based prevention strategies for MRSA transmission and infection are needed.