There are several causes of small bowel contamination. The effects of the long-term proton pump inhibitor treatment on the development of bowel symptoms and/or small intestinal bacterial overgrowth have been highlighted only in the past decade. The main diagnostic method is the hydrogen breath test that gives quantitative results with a simple, non-invasive procedure. There is a limited number of publications in the literature about the effects of proton pump inhibitor drugs on bowel bacterial milieau. Our results based on the investigations of two medical centres in Budapest show consistency with international data: the positive hydrogen breath test was present in 21% of the population using long-term proton pump inhibitors. In uncomplicated cases, symptom-free condition could be reached with probiotics, whereas in long lasting, chronic small intestinal bacterial overgrowth, antibiotic treatment should be considered. Rifaximin, a non-absorbable antibiotic showed high efficacy in the treatment of small intestinal bacterial overgrowth, with fewer side effects compared to systemic antibiotics.