Root extract from Pelargonium sidoides DC is used therapeutically as antimicrobial agent against infections of the respiratory system. In order to elucidate possible modes of actions we investigated the influence of P. sidoides root extract on microbial adhesion with Helicobacter pylori as model microorganism, a germ with a strong adherence to human stomach tissue. In an in-situ anti-adhesion assay intact human stomach tissue from patient resectates was incubated with fluorescent-labelled bacteria. Epithelial adhesion occurred in untreated samples and was quantified by fluorescent microscopy. Pre-treatment of the bacteria with Pelargonium extract showed good anti-adhesive activity. The antiadhesive effect was clearly dose-dependent in a range from 0.001 to 10 mg/ml. Within agar diffusion-test the extract had no direct cytotoxicity against H. pylori. The results show that the root extract from Pelargonium sidoides is a potent anti-adhesive agent against H. pylori and could therefore be a useful choice to avoid the first step of a bacterial infection.