Despite advances in the husbandry of nonhuman primates, natural and experimentally induced diseases continue to pose risks to animal health. These risks are particularly important when such disease results in immunodeficient states that provide an opportunity for the development of opportunistic infections. Because opportunistic agents may serve as significant confounders to research and hold potential for zoonotic transmission, knowledge of disease pathogenesis, surveillance, and risk reduction is particularly important to individuals who work closely with primates. Endogenous diseases of primates that result in blunted immune responses and thus allow for the development of opportunistic infection include simian type D retroviruses and measles. In addition, simian immunodeficiency virus is a frequently studied experimental cause of immunosuppression. This article focuses on clinical and pathological aspects of the most common opportunistic infections that occur in nonhuman primates maintained in research settings. The complete elimination of all infectious agents from primate colonies may be impossible and unwarranted, but microbial surveillance programs can help both to define the complement of agents present in a colony and to elucidate their potential impacts on colony health, zoonotic risk, and experimental research. We discuss risk reduction through the use of quarantine procedures, specific pathogen-free animals, and environmental controls.