Water supply contamination has been considered as a risk factor for the spreading of Mycobacterium avium subsp. paratuberculosis (Map) among the dairy cattle population in North-eastern Italy, where the herd level prevalence of infection has been estimated to be ~27%. The Monti Lessini area of Verona province is characterised, as most of the alpine territory, by the use of alpine pastures in the summer season. These 6,290 hectares of pastures, woods and rocks have been historically divided in 92 portions called "malga", in which cattle from different herds and ages graze from May until September. To estimate the risk of Map spread through natural and artificial ponds, which are the principal source of water due to the soil structure, a PCR-based survey was carried out in 2003-2004. Water samples were collected from the same pond in different periods: in spring just after the thaw, in summer while cows were present and at the end of the grazing season when the animals left the mountain. A questionnaire was submitted and laboratory results, when present, recorded for each of the 35 herds involved in the study. Map insertion element IS900 was demonstrated in the water of 8 out of 15 "malga" but only in 11 of the 100 samples. Descriptive analysis of the herds' health status, ages and structure, geographical information on the pastures, temporal pattern of sample collection and presence of wild animals are considered in relation to water results. These findings provide some assurance that water contamination in alpine pastures is a minor risk factor for the transmission of Map infection. Nevertheless positive results obtained in the spring season suggest a role of wild ruminants and lagomorphs in the epidemiology of paratuberculosis in the south-eastern Alps.