Faecal samples from 230 diarrhoeic and healthy calves aged 0-6 weeks, from 100 farms in Austria, were examined between October 2004 and February 2005 for the presence of bacteria, especially Shiga toxin-producing Escherichia coli (STEC), viruses and parasites. Escherichia coli was detected in 17% of all the faecal samples and was more prevalent in healthy calves. However, E. coli F5 was identified only in one calf without diarrhoea. Overall, 35 out of the 230 (15.2%) samples analyzed carried the Shiga toxin gene: stx1, stx2 or both stx1 and stx2 in their faeces, STEC. Nevertheless, out of 39 pathogenic E. coli positive samples observed, only two carried the Shiga toxin genes: stx1, in a diarrhoeic calf and both stx1 and stx2 in a healthy calf. eaeA and Ehly genes were detected more frequently in the strains from diarrhoeic calves 57.1% and 50.0%, respectively. Clostridium perfringens was detected in twenty-one samples, the most prevalent toxin type of Clostridium perfringens was found to be type A (76.2%). Other bacteria such as Klebsiella spp. and Proteus spp. were present in 1.3% and 0.4% of all samples. Salmonella spp. was not detected. The detection rates of other enteropathogens were 25.7% bovine coronavirus, 11.7% Cryptosporidium spp., 10.4% Eimeria spp., 9.1% group A rotavirus and Giardia spp. 6.1%. We demonstrated the presence of the STEC virulence genes in healthy and diarrhoeic Austrian calves but the importance of the virulence factors of STEC (stx1, stx2, eae and Ehly) in calf diarrhoea and systemic disease is not well defined. Therefore, further studies are necessary to identify reservoirs or potential sources of virulent STEC strains in order to establish control and prevention strategies for STEC associated diseases in animals and humans.