A survey was undertaken to determine the microbiological status of Australian wheat and the distribution of microorganisms in the flour milling fractions and end products. A total of 650 milling process and end product samples was obtained from nine flour mills located in New South Wales (4), Queensland (2), Victoria (2) and Western Australia (1) during the 1997-1998 and 1998-1999 wheat seasons. Most frequent (modal) counts in wheat and flour were, respectively, as follows: aerobic mesophilic plate count, 10(5) and 10(2) colony forming units/gram (cfu/g); coliforms, 10 and 1 most probable number/gram (MPN/g); Bacillus spp., 10(4) and 10(2) cfu/g; B. cereus, 1 and 0.1 MPN/g; mesophilic aerobic spores, 10 and 1 cfu/g; aerobic thermophiles, both 10 cfu/g; yeasts, 10(3) and 10(2) cfu/g, and moulds, 10(3) and 10(2) cfu/g. Bacillus spp., coliforms, yeasts and moulds were the most frequently detected microorganisms throughout the survey. The most common moulds isolated were Aspergillus, Penicillium, Cladosporium and Eurotium spp. Environmental serovars of Salmonella were isolated from two samples. Escherichia coli and B. cereus were present at very low levels, a majority of positive samples being at the minimum level of detection (3 and 0.3 MPN/g, respectively). As wheat grain layers are separated, surface-adhering contaminants are concentrated in end product bran, wheat germ and pollard, which comprise the outer layers of the grain. Consequently, the inner endosperm fraction contains lower microbial counts, and flour is the cleanest end product of the milling process. Higher microbiological counts midstream in the milling process indicate that equipment contamination may contribute to microbiological contamination; however, the microbiological quality of incoming wheat has a strong influence on the ultimate quality of milling end products.