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Amphipods of Diporeia spp. have declined considerably during the last decade in the Great Lakes. We examined the possibility that disease may be affecting these populations. A histological survey assessed the parasites in species of Diporeia within Lakes Huron and Michigan, USA, and the host response to some of them and to unknown factors. Amphipods were found to have an intranuclear inclusion body, and were hosts to a rickettsia-like organism, fungi, a haplosporidian, a microsporidian, epibiotic ciliates, a gregarine, a cestode, acanthocephalans and nodule formations. Epibiotic ciliates were most common (37% prevalence of infection), but a microsporidian (3.8%), a rickettsia-like organism (1.6%), fungi, including a yeast-like organism (1.3%), worms (1.3%), and a haplosporidian (0.7%) are likely associated with mortalities or detrimental effects on the host. The role these agents may have played in the decline of Diporeia spp. in the Great Lakes over the last decade is not clear. Interrelationships with the dynamics of various physical and biological factors such as high sedimentation, diminished food supplies, and virulent parasites could synergistically cause the decline in Diporeia spp. populations in Lakes Michigan and Huron.