Information on the prevalence of gastrointestinal nematodes (GIN) and protozoal parasites of alpacas in the United States is limited. A coprological survey was performed to determine the types of parasites, infection levels, and effects that seasonal changes had on the prevalence of GIN and protozoal parasites in alpacas located mainly in Indiana. From April 2009 through February 2010, 809 fecal samples were collected from eleven farms. One hundred forty-three alpacas had feces collected every other month for use in centrifugal flotation, while a subset population comprised of 99 alpacas had fecal egg and oocyst counts performed with the Modified McMaster technique using Sheather’s sugar solution. A 61-question questionnaire was submitted to the owners regarding husbandry practices currently in use. For the months April, June and August, results of pooled coprocultures revealed the presence of the trichostrongyles Haemonchus, Trichostrongylus, Oesophagostomum, Cooperia and Teladorsagia. Haemonchus was present in all coprocultures and was the predominant worm in nine of the eleven cultures. Seasonal variations of the infective third-stage larvae (L3) could not be determined due to low trichostrongyle fecal egg counts in the fall and winter months. At the farm level, trichostrongyle type and Nematodirus spp. eggs were the most prevalent (both 100%) followed, respectively, by Strongyloides papillosus eggs (90.9%), Trichuris spp. eggs (81.8%) and capillarid type eggs (54.5%). A farm was considered positive when a single alpaca was found having a positive fecal exam at any point during the course of the project. Two types of protozoal parasites were detected among the herds. Eimeria spp. oocysts (excluding Eimeria macusaniensis) were the most prevalent (100%), while Giardia spp. were found in 45.4% of the herds. Although it is an Eimeria species, E. macusaniensis was singled out from other Eimeria spp. based on its distinctive morphology, and was found to be present in 72.7% of the herds. At the alpaca-level prevalence, significant differences occurred seasonally for the trichostrongyles, Nematodirus spp., S. papillosus and Eimeria spp. Significant differences in logarithmically transformed mean fecal egg and oocyst counts occurred seasonally for the trichostrongyles and Eimeria spp. Mean fecal egg and oocyst counts for trichostrongyles and Eimeria spp. had a significant positive correlation with temperature, while S. papillosus had a significant positive correlation with precipitation. The prevalence of alpacas infected with Eimeria spp. and S. papillosus had a significant positive correlation with temperature, while Giardia spp. had a significant positive correlation with precipitation. The seasonal patterns of infection found in this study identifies seasons that alpacas may need deworming due to gastrointestinal (GI) parasitism, thus reducing the frequency of dewormer exposure on GI parasites and delaying the development of anthelmintic resistance.