Patterns of infection and prevalence result from complex interactions between hosts and parasites, the effects of which are likely to vary by species. We investigated the effects of age, sex and season on the likelihood of individual infection, and the effects of host population size, sex ratio and age structure on parasite prevalence. We capitalized on data from a long-term study of yellow-bellied marmots Marmota flaviventris potentially infected with fecal–orally transmitted intestinal parasites (Ascaris sp., Eimeria spp. and Entamoeba sp.), ectoparasitic fleas Thrassis stanfordi, and a flea- and louse-transmitted blood parasite Trypanosoma lewisi. Patterns of individual- and group-level infection varied widely by parasite. Yearlings were more likely to be infected with Tr. lewisi and Ascaris. Yearlings were also slightly more likely than adults to have Eimeria, but female yearlings had higher infection levels than female adults, while male yearlings had lower infection levels than male adults. Entamoeba infection decreased as the season progressed. Adults and males were more likely to be infected with Th. stanfordi. Ascaris prevalence increased with colony size. There were no significant relationships between colony size and prevalence of Entamoeba, Tr. lewisi, Eimeria or Thrassis. There was a small, but significant positive correlation between male-biased sex ratio and prevalence of fleas. The host population's age structure affected the prevalence of infection of Ascaris and Eimeria. Overall intestinal parasite diversity increased with colony size. Taken together, our results show a great deal of variation in the likelihood of individual infection and patterns of parasite prevalence in marmots.