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Group B Streptococcus (GBS) is a leading cause of morbidity and mortality in newborns worldwide. From 2000-2008, national guidelines in Germany recommended intrapartum antibiotic prophylaxis for pregnant women displaying risk factors (e.g. perinatal anogenital GBS colonization, rupture of the membranes ≥ 18 hours before birth), for the vertical transmission of GBS to their children.In 2008, these guidelines were revised in order to advocate universal, culture-based screening for GBS colonization among all pregnant women between 35 and 37 weeks of gestation. For the period 2009-2010, our prospective active surveillance study assessed the incidence of invasive GBS infections in infants aged 0-90 days in Germany. We did this by means of a capture-recapture analysis of two separate, independent systems (pediatric reporting vs. laboratory reporting). We compared our results with those from a previous study by employing an equivalent design (2001-2003). We detected a 32% reduction in GBS incidence, from 0.47 per 1,000 live births (n=679) in 2001-2003, to 0.34 per 1,000 live births (n=450) in 2009-2010. This decline primarily is tied to a reduced number of GBS cases in children under one week of age. In 2009-2010, the ratio of EOD to LOD reversed from 1.52 (206:136), as determined in 2001-2003, to 0.75 (92:122). This study is the first to assess changes in the incidence of invasive GBS in Germany after the implementation of the guidelines for intrapartum prophylaxis for pregnant women colonized with GBS.