In recent years, hospital infections caused by opportunist micro-organisms in immunosupressed patients groups have become increasingly important. These micro-organisms grow easily in water distribution systems even to the extent of producing bio-film. In the present study the aim was to determine microbial populations in water samples collected from the distribution system of a big hospital. Water samples were collected from one hundred different points around the water distribution system in different sections of the hospital. To analyse the water a membrane filter method was used. In eighty-four samples heterotrophic bacteria were isolated. The most frequent bacteria determined were Bacillus spp. (77%), Bacillus cereus (11%), Pseudomonas spp. (5%) and Staphylococcus spp. (4%). In fifteen samples more than one species of bacteria were isolated. In fifty-one samples, sixteen species of fungi were isolated, the most frequent being Penicillium spp. (24%), Aspergillus spp. (8%) and Acremonium spp. (5%). In thirteen samples more than one type of fungi was determined. In only six samples was no growth of fungi or bacteria observed. Over all the one hundred samples the counts of heterotrophic bacteria were not significantly correlated with the filamentous fungi counts (rs = -012, p = 0.05). Differences in the level of isolation or the concentration of bacteria and fungi between water from three old buildings and water from four new buildings were not significant (p > 0.05).