The role of water temperature and altitude of the river sites on distribution, prevalence and infection intensity of Tetracapsuloides bryosalmonae infected salmonids was investigated. The study is based on a 6 year survey of salmonids, mainly brown trout, Salmo trutta from 2000 to 2006 at 287 sampling sites across Switzerland. Almost 7000 fishes were tested for the presence of T. bryosalmonae by histological and immunohistochemical techniques. A good correlation between altitude and water temperature in Swiss rivers could be demonstrated. Therefore, the relation between altitude and sites tested for T. bryosalmonae infected fishes was investigated since water temperature values from these sites were not available. Percentage of sites with positive (infected) fishes was identical for altitudes between 200 and 800 m above sea level (m a.s.l.), while above 800 m a.s.l. only three sites with infected fishes were recorded. Site-specific prevalence values ranging from 0 to 100% and infection intensities from 0 to 6 were found over the whole altitude range from 200 to 800 m a.s.l., and no correlation with altitude was found. Conditions at altitudes >800 m may not be favourable for the establishment of the infection in fishes. With rising temperatures due to climatic changes, however, the prevalence of T. bryosalmonae infected fishes in altitudes >800 m a.s.l. could increase.