The aim of this study was to estimate the prevalence of helminthes and Eimeria in alpacas of two communities in Ocongate, Cusco, Peru, and to determine the association between the presence of these parasites with location, ecosystem, age and sex. A total of 1001 faecal samples were collected from Huacaya alpacas, 521 in the Pampacancha community and 480 in Mahuayani community during the end of the dry season (September-October 2011). Samples were analyzed by the sedimentation and flotation techniques with Sheather and Willis solutions. The parasite load was determined by the modified McMaster technique. Helminth genus was identified through the eggs, stool culture and infective larvae. Eimeria identification was done by oocyst sporulation. The prevalence was 68.4 and 61.5% for helminthes and Eimeria respectively. The multiple logistic regression tests showed a significant association between helminthes and age and between Eimeria and age and location (p<0.05). Parasites of the following genus were found: Nematodirus, Trichuris, Capillaria, Lamanema, Cooperia, Ostertagia, Trichostrongylus, Oesophagostomum, Bunostomum and Moniezia, where Nematodirus was the most frequent (p<0.05). Eimeria alpacae was the most frequent Eimeria (42%). The nematode load varied between 59.3 to 70.9 eggs per gram of faeces (epg) and Eimerias showed a geometric mean of 216 oocysts per gram of faeces (opg), both of them are considered of low level of parasite load.