Helicobacter pylori infection has been implicated in the development of peptic ulcer disease in children. Although clinical protocols for the diagnosis and treatment of this infection in children are available, the implementation of those guidelines by primary physicians are insufficient. In this study, we surveyed the clinical practices of 409 primary physicians who practice in West Virginia and treat children with H. pylori infection. Results showed in contradiction with the recommendation, primary physicians are still using serology as the preferred diagnostic method for this disease. Most of the physicians treat this disease with a combination of two antibiotics and anti-acid medication (H2 blockers or PPI) for at least one week. We conclude that an increase in knowledge of those guidelines among primary physicians may improve physicians' compliance with H. pylori guidelines.