Endemic infection with Helicobacter spp. is frequently detected in research mice colonies. So far, several species have been isolated including H. hepaticus, H. bilis, H. muridarum, H. typhlonicus and H. rodentium as the most prevalent ones. The transmission of this pathogen is through fecal-oral route, followed by persistent long-term shedding in infected individuals. In immunocompetent mice the infection is subclinical, however, emerging evidence show that it can have significant health implications leading to typhlocolitis, intestinal and hepatic tumors and mammary gland neoplasia. Moreover, the infection alters reproduction successes with increase in fetal resorptions, decline in neonatal weight and decreased number of weaned pups detected in both experimentally and naturally infected mice. In addition to the impact on animal health and welfare, the infection might have confounding effects on obtained research results; therefore, regular screening and eradication are key for obtaining a pathogen free colony. In order to eliminate a naturally acquired Helicobacter infection in our animal facility, we have attempted an eight-week long treatment protocol with amoxicillin, clarithromycin, metronidazole and bismuth, administered in drinking water. This treatment route is more economical, time-efficient and noninvasive compared to other alternatives for eradication such as treatment with medicated diet, oral gavage or cross fostering. To determine the results of the administrated therapy we have performed qPCR of DNA extracted from fecal pellets