To study the association of Helicobacter pylori with peptic ulcer and the associated histopathological changes, to characterize the isolated strains in terms of their protein profile, 83 peptic ulcer cases were studied. A high association of H pylori with peptic ulcer (duodenal ulcer 77%, gastric ulcer 75%) and gastritis (74%) was observed. Age and smoking did not have any relationship with H pylori infection. The infection was predominantly associated with the 'quiescent' form of chronic gastritis. Comparative sodium dodecyl sulfate polyacrylamide gel electrophoresis of whole cell extracts of the local isolates and a reference strain from Australia showed a general homogeneity between the strains with obvious interstrain differences. However, the difference between the local isolates and the reference strain was more marked. Significant association of H. pylori with peptic ulcer along with strain variations were observed.