Antibiotic resistance in nosocomial infections is an ever-increasing problem as health care institutions provide care for children with more complicated medical and surgical problems. Several mechanisms of antibiotic resistance are reviewed for both gram-negative and gram-positive nosocomial pathogens. These adaptive resistance mechanisms allow organisms to survive in an environment of extensive antibiotic use and result in clinically significant infections. Mobile genetic elements have facilitated the rapid spread of antibiotic resistance within and among species. The clinical challenge faced by many practitioners is to understand these mechanisms of antibiotic resistance and to develop strategies for successfully treating infection caused by resistant pathogens. Nosocomial outbreaks caused by resistant organisms are described, and an approach to empiric therapy based on presumed pathogens, site of infection, and local resistance patterns is discussed.