The size distribution of viral DNA in natural samples was investigated in a number of marine, brackish and freshwater environments by means of pulsed field gel electrophoresis (PFGE). The method was modified to work with both water and sediment samples, with an estimated detection limit for individual virus genome size groups of 1-2 x 10(4) virus-like particles (VLP) mL(-1) water and 2-4 x 10(5) VLP cm(-3) sediment in the original samples. Variations in the composition and distribution of dominant virus genome sizes were analyzed within and between different habitats that covered a range in viral density from 0.4 x 10(7) VLP mL(-1) (sea water) to 300 x 10(7) VLP cm(-3) (lake sediment). The PFGE community fingerprints showed a number of cross-system similarities in the genome size distribution with a general dominance of genomes in the 30-48, 50-70 and 145-200 kb size fractions, and with many of the specific genome sizes detected in all the investigated habitats. However, large differences in community fingerprints were also observed between the investigated sites, and some virus genome sizes were found only in specific biotopes (e.g. lake water), in specific ecosystems (e.g. a particular lake) or even in specific microhabitats (e.g. a particular sediment stratum).