Background: The idiopathic peptic ulcers (IPU) or non-Helicobacter pylori, non-steroidal anti-inflammatory drug non-NSAIDs associated peptic ulcers are a serious therapeutic challenge. The prevalence of IPU is increasing in some parts of the world. Objectives: This study aimed to determine the prevalence of IPU in southeastern Iran. Methods: In this cross-sectional study, a total of 367 patients with active peptic ulcer were diagnosed by endoscopy between Jan 2018 and Feb 2019. The patients were assessed for history of medication use (including NSAIDs) in the past month, smoking, alcohol, as well as a complete history of health problems related to underlying disease such as cardiopulmonary, hepatic, renal problems, and chronic pancreatitis. Biopsy samples from antrum were performed for rapid urease test (RUT), and if RUT was negative, then biopsies were sent for histopathology. If both RUT and pathologic findings were negative for H. pylori, in patients who had treatment for H. pylori eradication, anti-H. pylori IgG antibody of blood samples was assessed. Patients were considered infected with H. pylori if any of the diagnostic tests had a positive result. Results: According to the results, 336 (91.3%) cases had at least one of the two main etiologic factors (H. pylori and NSAIDs) for peptic ulcer. While 323 (87.7%) patients were H. pylori-positive, 45 (12.3%) patients were H. pylori-negative. However, out of 45 H. pylori-negative cases, 13 patients had a positive history of using NSAIDs, and 32 (8.69%) patients were IPU. Conclusions: Our study showed that both H. pylori infection and NSAIDs use remain the main cause of peptic ulcers, and the prevalence of IPU is relatively high in Zahedan.