In mountainous areas, where small ruminants form an integral part of livestock farming, an effective control of parasites is of high importance, because the animals are grazing on communal pasture land during the summer months. But knowledge on the infection status of the animals, which is needed for an effective control, is very limited in these areas. Therefore, this study aimed to assess the prevalence of endoparasitic infections and the use of preventive measures in sheep and goat farms in South Tyrol, a mountainous region of Northern Italy. A questionnaire was used to collect information on farm structure and management as well as routine parasite control measures. Following the survey, a total of 3536 individual fecal samples from 123 sheep and goat flocks were analysed over three periods in autumn 2015, spring and autumn 2016 with routine methods including fecal egg counts (FEC) and oocysts counts (FOC). Animals were classified into <6 months, 7–12 months and >12 months of age. Goat flocks had an average herd size of 31 (range 5–125) and sheep flocks of 28 animals (range 2–100). Mountain sheep and goat breeds were dominant. More than 60% of the sheep and 40% the goat flocks were grazed on communal summer pastures at altitudes >1500 m a.s.l. Both sheep and goat farmers perceived gastrointestinal strongylid nematodes (GIN) as the most frequent parasites. Only 16% of the sheep and 30% of the goat farmers ever before this study did coprological examinations. More than 90% of the farms applied anthelmintic treatments; usually once (sheep: 32%, goats: 53%) or twice (sheep: 68%, goats: 42%) per year. Independent of the season, macrocyclic lactones were the most commonly used anthelmintics. More than 30% of the sheep-12 months and 16% >12 months were GIN-negative. Sheep <6 months had a lower FEC than animals of both other age classes (P < 0.05). In goats, 15.9% of the samples collected from animals <6 months were GIN-free. Age classes, however, did not differ for FEC in goats (P > 0.05). Third-stage larvae identified in coprocultures were dominated by Teladorsagia/Trichostrongylus in both sheep (56.5 ± 24.5%) and goats (60.5 ± 25.8%). While in sheep lambs had a higher FOC than both other age classes, kids did not differ from goats at an age of 7–12 months but only from those >12 months (P < 0.05). In sheep, tapeworms were found in around 13% in both groups below 12 months and 6.5% in sheep>12 months, while these parasites were identified in 18.5, 7.3 and 5.7% in goats <6 months, 7–12 months and >12 months, respectively. The prevalence of lungworms at flock level varied between seasons from 18 to 50% in sheep and 44–78% in goats. This first report on endoparasitic infections of sheep and goats in the mountainous region of South Tyrol reveals a high prevalence of endoparasites, especially GIN at a medium infection level, tapeworms and lungworms. Anthelmintics are regularly used, while fecal sampling for selective treatment only exceptionally. Therefore, parasite control measures should be optimized to reduce the risk for the development of anthelmintic resistance, which was already reported from neighboring regions.