Seven Danish rainwater systems were investigated with respect to the microbial water quality. The general microbiological quality (total numbers of bacteria (AODC)), and heterotrophic plate counts on R2A and Plate Count Agar in the toilets supplied with rainwater were approximately the same as in the reference toilets supplied with drinking water. However, in 12 of the 27 analysed samples one or more pathogens were observed (Aeromonas sp., Pseudomonas aeruginosa, Legionella non-pneumophila, Campylobacter jejuni, Mycobacterium avium, and Cryptosporidium sp.). These pathogens were not found in any of the reference toilets (32 toilets). This means that the use of rainwater introduced new,potentially pathogenic microorganisms into the households which would normally not occur in toilets supplied with water from waterworks. Furthermore, four graywater systems were investigated where water from the shower and hand wash basin was reused. The graywater systems gave more problems in terms of bad smell and substantially higher numbers of E. coli and Enterococcus in some toilet bowls supplied with graywater.