Soil samples were collected during January 1999 and 2000 from the ornithogenic soils of the Adelie penguin colony at Cape Bird, the volcanic soils at Cape Evans, the gravels and ornithogenic soils of Cape Royds, the western (upper) regions of the Miers Valley, the Canada Glacier site of special scientific interest at Lake Fryxell, Taylor Valley, the meltpools of the McMurdo Ice Shelf near Bratina ... Island and the area around Scott Base. Samples were collected with sterile transfer of surface and subsurface samples. Soil, water and atmospheric temperatures were monitored and recorded. In situ ATP analysis was used to measure soil microbial activity and microbial biomass in surface mineral soils of the Antarctic Dry Valleys, the Miers and Taylor Valley and they were compared with that of an ornithogenic soil at Cape Bird. The fatty acid content of soil samples was determined by gas chromatography analysis. Samples returned to the lab were tested with PCR methods to test for human enteric bacteria E.coli and Clostridium clostridiiforme as indicator organisms of human contamination and compared with pristine samples. Samples were also tested using PCR amplification of 16S rDNA and phylogenetic analysis.