The concentration and composition of fungal flora in dental unit waterlines (DUWL) were evaluated. For this purpose, water samples from unit reservoirs and high-speed handpieces, and biofilm from the waterline walls from units were collected. Subsequently, analogous samples from DUWL were taken before and after disinfection using agent containing hydrogen peroxide. In the examined samples, the yeast-like fungi Candida albicans and Candida curvata, Geotrichum candidum were found. The following species of mould were also identified: Aspergillus amstelodami, Aspergillus fumigatus, Aspergillus glaucus group, Aspergillus (=Eurotium herbariorum) repens, Citromyces spp., Penicillium (glabrum) frequentans, Penicillium pusillum, Penicillium turolense and Sclerotium sclerotiorum (Sclerotinia sclerotiorum). Before disinfection, Candida curvata and Candida albicans constituted the greatest proportion of the total fungi in the reservoirs water; in the water of handpieces - Candida albicans and Aspergillus glaucus group; and in the biofilm samples - Aspergillus glaucus group and Candida albicans. After disinfection, in all 3 kinds of samples, Candida albicans prevailed, constituting from 31.2-85.7% of the total fungi. The application of agent containing hydrogen peroxide caused a significant decrease both in the number of total fungi and individual fungal species, which confirms the product effectiveness in fungal decontamination of DUWL.