Between 1989 and 1998, 3,504 rodents of the genera Dipodomys and Perognathus were collected from 4 permanent collecting sites on the University of New Mexico's Long Term Ecological Research station, located on the Sevilleta National Wildlife Refuge (SNWR), Socorro County, New Mexico. All animals were killed and examined for endoparasites (acanthocephalans, cestodes, coccidia, and nematodes). The present report focuses on 3 endoparasite groups, cestodes, coccidia, and nematodes. Specific analyses address how prevalence changes were related to abiotic factors such as habitat, season, or precipitation, and how prevalence of each parasite species in each host species differed in relation to host age, host sex, host reproductive status, host body mass, host density, parasite–parasite interactions, and host specificity. A logistic regression was used to determine which host characters and which abiotic factors are correlated with a parasite infection. Significant variables for at least half of the parasites include season, site, and winter precipitation. However, no parasite prevalences were correlated, and significant variables were not identical between parasites, indicating that each parasite species varied independently and that no generalizations can be drawn. The parasite prevalences in these rodents on the SNWR vary in independent and complex ways.