Anaerobic bacteria can cause a variety of endogenous infections in children. Because of their fastidious nature, they are difficult to isolate from infectious sites, and are often overlooked. Anaerobic infections can occur in all body sites, including the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin, and soft tissues. They colonize the newborn after delivery and have been recovered from several types of neonatal infections. These include cellulitis of the site of fetal monitoring, neonatal aspiration pneumonia, bacteremia, conjunctivitis, omphalitis, and infant botulism. The lack of adequate therapy may lead to clinical failures. Their isolation requires appropriate methods of collection, transportation and cultivation of specimens. Treatment is complicated by their slow growth, their polymicrobial nature and their growing resistance to antimicrobials. Antimicrobial therapy is often the only form of therapy required, whereas in others it is an important adjunct to a surgical approach. Because anaerobes are generally recovered mixed with aerobic organisms, the choice of antimicrobial agents should provide coverage of both types of pathogens.