The purpose of this study was to compare the determination of antigen in stool for diagnosis of Helicobacter pylori (Hp) with invasive methods in cases diagnosed as gastritis and duodenal ulcer in terms of etiopatology and to evaluate the effect of this method in Hp eradication in the post treatment follow-up. Eighty patients in the age range of 23-86 with dispepsia compliments admitted to gastroenterohepatology outpatient clinics of two different centers were prospectively included in this study. All patients had received the diagnosis of chronic gastritis or gastritis or duodenal ulcers by endoscopy. Four tissue samples were obtained during endoscopy for culture, urease determination, pathological investigation and polymerase chain reactin studies. Additionally, Hp stool antigen (HpSA) was investigated in all patients HpSA E A (Meridian Diagnostic, USA) test kit. Helicobacter pylori was considered as positive when only culture was positive or two out of three invasive test methods were positive. Positive cases were treated with three antibiotics (omeprazol+amoxicilin+claritromicin) for seven days. Fortyfive patients who could be followed one month after treatment underwent invasive tests and HpSA test again. Out of 50 Hp (+) cases, according to the criteria of this study, in 46 (92%) HpSA were detected (sensitivity 92 %). Out of 30 Hp (-) cases in 27 HpSA was found negative (specificity 90 %). Out of 45 Hp (+) cases who had follow-up after treatment, in 37 (86.1%) infection was eradicated. Thirty five (94.6%) of these 37 cases had HpSA results negative whereas in seven cases out of eight having infection HpSA was detected positive (HpSA sensitivity after therapy 87.5%, HpSA spesificity after therapy 94%). This study emphasizes that HpSA test in stool samples is an accurate and simple method for identification of H. pylori infection. It is concluded that HpSA test can be used in checking bacteria eradication in post-treatment follow-up.