Gastric biopsy specimens from 156 adult patients from southern Estonia suffering from chronic gastritis, peptic ulcer disease, and perforated peptic ulcer were analyzed by PCR. The cagA gene was evenly distributed throughout 87% of the specimens from the patients with the different gastric diseases. The presence of the cagA gene correlated with that of vacA signal sequence type s1a (99%). However, no clear differences were found in the distribution of cagA and vacA genotypes among patients in Estonia with severe perforated peptic ulcer, uncomplicated peptic ulcer, or chronic gastritis.