Based on voluntary examinations for Salmonella in laying hen flocks in Germany, it was investigated whether a statistically significant trend in Salmonella prevalence could be observed in the period 2003 to 2007. Furthermore, it was studied whether the implementation of Regulation (EC) No 1168/2006 led to an improvement of the collected data and a change in the Salmonella prevalence in 2008. To compensate for differences in data availability, submitted data were weighted by regional laying hen population size and compared with results from the non-weighted data. Between the years 2003 to 2007 a significant reduction of Salmonella prevalence could be observed. Weighting of data by population size improved trend recognition for routine sampling results. This may point towards a real reduction of Salmonella prevalence in German layer flocks in the years till 2007. The obligatory implementation of the control programme in 2008 led to a remarkable increase of examinations performed and an increased frequency of detection of Salmonella in flocks of laying hens. This tendency was statistically highly significant (p<0,0042) for the overall dataset as well as for data from targeted sampling and other sampling. Again, after weighting data from routine sampling, a statistically significant (p<0.05) increase of Salmonella prevalence could be shown. The two dominant serovars in human salmonellosis, namely S. Enteritidis and S. Typhimurium were most frequently observed in German laying hen flocks with S. Enteritidis being much more recurrent than S. Typhimurium. It is obvious from the available data that a good data quality is the prerequisite for a realistic evaluation of the Salmonella situation and that weighting may compensate for some of the bias inherent in the data reporting system.