Introduction and Aims: Do H. pylori isolates from normal and dyspeptic patients have similar genetic profiles? Since genotype variation occurs within H. pylori population with high frequency, it is tempting to exploit techniques such as RAPD-PCR to examine the possible correlation between specific H. pylori genotypes and different peptic diseases. In this study, H. pylori isolates from different dyspeptic patients were genotyped by RAPD-PCR. Materials and Methods: H. pylori isolates from 66 patients, 41 normal, 21 with ulcer, and 4 with cancer were cultured, DNAs were extracted by phenol-chloroform. RAPD-PCR was optimized, using 10-nt primers of arbitrary sequences (1281, 1254, 1247) and isolate-specific fingerprints were generated. Analysis of PCR products on agarose gel was performed using NTSYSpc program. Dendrograms were calculated according to Jaccard & Nei. Results: According to differences in genetic profiles, H. pylori isolates were clustered into 4 distinct groups: 2 groups consisted of isolates from normal patients, 2 groups of isolates from patients with ulcer, and isolates from patients with cancer were clustered along with isolates from normal and ulcer patients. Furthermore, isolates from ulcer patients appeared in the cluster related to isolates from normal patients. Conclusions: Genetic variation is quite frequent within H. pylori populations; thus RAPD-PCR is an effective technique to reveal genetic diversity of isolates from different dyspeptic patients. In this study, H. pylori strains were clustered into 4 groups: 2 groups from normal patients, and 2 from patients with ulcer. Further studies in larger populations will help to correlate a certain peptic disease to specific strain of H. pylori.