Nematode, cestode, protozoan, microsporidian, and pentastomid parasites affect domesticated and wild rabbits, hares, and jackrabbits of the genera Brachylagus, Lepus, Oryctolagus, Pentalagus, and Sylvilagus. Some endoparasite infections are of limited or no significance, whereas others have potentially profound consequences. Accurate identification of endoparasites of rabbits, hares, and jackrabbits is an important facet of the work of veterinary pathologists engaged in lagomorph pathology. Here I review endoparasites from the pathologist’s perspective, focusing on pathogenesis, lesions, and implications of infection. Stomach nematodes Graphidium strigosum and Obeliscoides cuniculi are infrequently pathogenic but may cause gastritis and gastric mucosal thickening. Nematodes Passalurus ambiguus, Protostrongylus spp., Trichostrongylus spp., and Trichuris spp. are rarely associated with disease. Adult Capillaria hepatica (syn. Calodium hepaticum) nematodes and non-embryonated eggs cause granulomatous hepatitis in wild Oryctolagus cuniculus and Lepus europaeus, resulting in multifocal, off-white, hepatic lesions, which may be misdiagnosed as hepatic eimeriosis. When the rabbit is an intermediate host for carnivore cestodes, the space-occupying effects of Cysticercus pisiformis and Coenurus serialis may have pathologic consequences. Eimeria stiedai is a major cause of white-spotted liver in O. cuniculus, particularly in juveniles. Enteric coccidiosis is a noteworthy cause of unthriftiness in young animals, and frequently manifests as diarrhea with grossly appreciable multifocal off-white intestinal lesions. O. cuniculus is the natural host for the zoonotic microsporidian Encephalitozoon cuniculi. Infection may be acute and focused mainly on the kidneys, or it may follow a chronic disease course, frequently with neurologic lesions. A latent carrier status may also develop.