Patients with advanced human immunodeficiency virus (HIV) infection who are severely immunosuppressed develop a variety of opportunistic infections that have a significant impact on their well-being, quality of life, health-care costs, and survival. The risk for development of opportunistic infections depends on exposure to potential pathogens, the virulence of the pathogens, the degree of host immunity, and the use of antimicrobial prophylaxis. Many studies have confirmed the benefits of prophylaxis in severely immunosuppressed patients. Factors that affect the use of prophylaxis for prevention of opportunistic infections in HIV-infected patients include the prevalence and potential severity of the disease, ease of treatment if infection occurs, the cost-effectiveness of the prophylactic regimen, and the potential for increased survival, drug toxicity, drug interactions, and emergence of resistance with the regimen. The United States Public Health Service and the Infectious Diseases Society of America (USPHS/IDSA) have established disease-specific recommendations for use of prophylaxis for opportunistic infections in HIV-infected patients. These guidelines identify regimens that are strongly recommended as standards of care, regimens that should be seriously considered in selected patients, and regimens that are not routinely indicated but may be considered in selected patients. Although further study is needed, advances in antiretroviral therapy may have an important impact on the recommendations for prophylaxis and may eventually allow discontinuation of these regimens in patients who regain functional immunity.