The program package "Integrated Bulletin for Infectious disease Surveillance for Schleswig-Holstein" (IBIS(SH)) was introduced in 2008 for the automated data analysis of notifiable infectious diseases in Schleswig-Holstein, Germany. The Java-based IBIS(SH) software supports access to the national SurvNet@RKI reporting data via Access and MS SQL. The aim of the IBIS(SH) system is early warning and interpretation of clusters and monitoring of trends. One module of the system permits the analysis of temporal aberration by comparison of data from previous years. The interpretation system is based on the weekly median and on percentile values from previous years. The extent of an aberration is assessed by a five-step score magnitude scale. Another module permits the detection of regional clusters by the weekly assessment of a population-based risk analysis. IBIS(SH) automatically generates tables and graphs for the weekly bulletin and their allocation in the Internet. Data for the most relevant pathogens in Schleswig-Holstein are presented for the year 2009. The performance of the automated temporal and the regional detection systems are compared to outbreak detection by local health authorities.