Shiga toxin producing Escherichia coli (STEC) in sewage influent into surface water are a potential source of human infections with STEC. Eight sewage treatment plants in Bavaria, Germany, were sampled at regular intervals from 2003 to 2004 in order to estimate STEC load and quantify risk factors. 95 of 378 samples (25 %) were tested positive for stx1and/or stx2 with PCR after enrichment culture. STEC elimination after treatment was 44 %. The following risk factors were analysed with logistic regression: location of sewage plant (rural vs. urban), treatment plant technology (two stage vs. three stage treatment) and sampling location (sewage input vs. sewage output). Rural plants had odds-ratios of 1,7 (95 % CI 1.03 - 2.69; p = 0.038) for a positive stx1 and/ or stx2 PCR result, sampling at sewage input of 2.1 (95 %CI 1.28 - 3.36; p = 0.003) and three stage plants of 1.51 (95 % CI 0.94 - 2.44; p = 0.087, not significant). Sampling after rain and after dry spells had no impact on STEC abundance (univariate Chi-square test = 0.01; df1; p = 0.920). Rural sewage plants had higher odds of STEC content. The influence of the sewage plant technology on the STEC load requires further clarification.