This study examined bacterial contamination levels from 47drinking water sources(92%were surface sources)from two rural Ugandan villages using EC 3M TM petrifilmsTM incubated for 24 h at 37ºC. E. coli counts in 1ml water samples ranged from 0-120 cfu/ml. Confirmation of presumptive E. coli was performed by transferring colonies onto Blood agar followed by characterization by subculture on selective media and standard biochemical analysis. Selected isolates were verified by sequencing of their 16S rRNA genes. A total of 184 colonies were isolated from petrifilms representing 70%of the water sources and 92% of the isolates were identified to genusl evel (n=169). Only 24%of presumptive E. coli, isolates were confirmed as E. coli (n=40). Additionally 61%of isolates were found to be lactose negative and were confirmed as Salmonella, Yersinia and Proteus (n=103). Purified bacterial isolates from the Ugandan water samples and laboratory strains were replated on new petrifilms at various dilutions to determine the potential for misclassification of colony color or gas production. Upon inoculation of new petrifilms, misclassification of coliforms was observed. While the level of bacterial contamination in the rural Ugandan drinking water sources is not unexpected, isolation of lactose negative bacteria from presumptive E. coli colonies and misclassification of coliforms by the petrifilms was unexpected.