The aim of the study was to identify key decision points in the management of Helicobacter (H.) pylori-associated diseases by general practitioners (GPs) in Bosnia and Herzegovina (BH), in relation to standard protocols. A questionnaire especially designed for this survey was distributed to 500 randomly selected primary health care physicians in Bosnia and Herzegovina. Two hundred and sixty-four of them responded (response rate 53%), and their answers were included in the study and analyzed. It appears that the most important source of information about H. pylori management were pharmaceutical industry-sponsored symposia (53%). The main obstacle in the application of full-scale worldwide accepted diagnostic and therapeutic protocols was the lack of inexpensive and easy-to-get diagnostic test. Seventy-one percent of GPs treated H. pylori infection in their practice. Of those who prescribed eradication therapy only 9% had the evidence of infection by rapid urease test before starting eradication. More than two-thirds of the surveyed GPs prescribed H. pylori eradication therapy, but only one tenth based such therapeutic decision on the positive evidence for the presence of H. pylori infection because of the lack of proper laboratory test.