Extensive alpaca farming in the Colca Valley (Arequipa, Peru) is the most important resource for farmers who live in this remote area of the country. Grazing is the major available source of food, whereas forage production and supply are limited. Food availability is low during the dry season predisposing animals to parasitic diseases and reproduction failure. In this study, we looked into gaining an overview about flock health management and nutritional and parasitological status of different age groups in medium-large alpaca farms at the beginning of the dry season. A total of 20 herds were included in the survey and 288 fecal samples were collected and analyzed to determine prevalence and oocysts/eggs output level of the most common gastro-intestinal parasites that affect alpacas. Body condition scoring (BCS), was used to determine the nutritional status of sampled animals, belonging to different physiological classes (i.e. crias, tuis, lactating females, non-lactating females, males). Coccidiosis was the parasitic disease with the highest prevalence and output level. It was the most relevant parasitic disease in all classes and especially in young pre-breeding animals. Higher burdens were found in subjects with lower BCS. More specifically, the farms with higher cria mortality rates showed also a tendency to have higher prevalence values of Eimeria macusaniensis . An improved management of nutritional aspects and parasite control, in particular regarding the weaning phase, is expected to enhance the farming reproductive and productive performances of the alpacas in this region.