The aim of this study was to determine the prevalence of Eimeria spp in alpacas of two communities of the Macusani district, Carabaya province, Puno, Peru, during the dry season, accodring to origin, age (5 month to <1 year, 1-3 years, >3 years) and sex. Coprological samples (n=1319) were collected from Huacaya alpacas (598 from the Hatun Phinaya community and 721 from the Queracucho community) during August and October 2010. Samples were analyzed by qualitative techniques (sedimentation and flotation using Sheather and Willis solutions). The quantification of Eimeria load was done using the modified McMaster method and the oocyst sporulation and measurement was done to identify the species of eimerias. The results showed a prevalence of 52.4% for Eimeria spp. Risk analysis by multiple logistic regresion test showed alpacas of 5 months to <1 year and those of 1 to 3 years had 13.2 and 2.4 times higher risk to become infected to Eimeria sp than those over 3 years (p<0.05). Five Eimeria species were identified, where the frequency of large eimerias was 8.7% for E. macusaniensis and 0.7% for E. ivitaensis. Among the small Eimeria species (E. punoensis, E. alpacae, E. lamae), E. punoensis showed the greatest frequency (66.2%). The parasitic load of eimeria was considered low (187.8 opg). These findings confirm that eimeriosis is a potential healthy problem in alpacas of the two Macusani communities.