Objective. Based on a large trial of Helicobacter pylori-positive peptic ulcer patients, we studied whether the size of the ulcer, along with other clinical and histological characteristics, has any effect on healing. We also studied the clinical and endoscopic characteristics associated with size of the peptic ulcer. Material and methods. A total of 333 consecutive patients with H. pylori infection and peptic ulcer were enrolled (mean age 54.8±12.7 years). Location of the ulcer was recorded by gastroscopy and the presence of H. pylori was assured by rapid urease test, histology and by serum H. pylori IgG and IgA antibody measurement. The diameter of the ulcer was measured by placing the opened biopsy forceps (7 mm) beside it. Biopsy specimens were examined in accordance with the Sydney system. Results. Mean size of the peptic ulcer was 13.2±8.3 in corpus, 11.3±5.3 in antrum, 13.8±7.8 in angulus, 9.5±5.3 in prepylorus and 9.2±4.7 mm in duodenum (duodenal versus gastric type; p<0.05). Average size of the ulcers was 9.4±5.3 mm in patients with Forrest III type and 11.5±6.8 in other types (p<0.05). Patients who were ≥50 years of age, currently smoking, or who had corpus-predominant chronic gastritis or atrophic gastritis, had larger ulcers than others. Size of index ulcers, successful eradication of H. pylori and the presence of atrophic gastritis were independent factors for healing. The odds ratio was 11.5 (95% CI 3.3–40.5; p<0.01) for eradication of H. pylori, 3.5 (95% CI 1.1–11.2; p<0.05) for size of the index ulcer (≤10 mm versus >10 mm) and 3.4 (95% CI 1.2–9.8; p<0.05) for atrophic gastritis versus no atrophy. Conclusions. Size of the peptic ulcer, successful H. pylori eradication and atrophic gastritis were independent factors for the healing of peptic ulcers. A number of clinical and endoscopic variables (age, current smoking, corpus-predominant gastritis, Forrest classification) were associated with size of the peptic ulcer in H. pylori-positive patients.