This randomized controlled study evaluated the association of Helicobacter pylori (H. pylori) with chronic periodontitis patients with and without type II Diabetes Mellitus. H. pylori is considered to be a pathogen responsible for gastritis, peptic ulcers and a risk factor for gastric cancer. The aim of the present study was to evaluate the association of H. pylori with chronic periodontitis patients with and without type II diabetes mellitus before and after treatment. The prevalence of H. pylori in periodontal pockets was determined by rapid urease test in a 36 patients, which were grouped as Group 1 (Healthy subjects), Group II (chronic periodontitis patients) and Group III (Chronic periodontitis patients with Type II Diabetes Mellitus), 12 in each group before treatment by collecting plaque samples. After treatment, 12 plaque samples were collected and prevalence H. pylori was detected. Group II and Group III had a significantly higher rate of positive results for H. pylori compared to healthy subjects before treatment. After treatment, H. pylori were not detected in Group II and in Group III Only one of 12 chronic periodontitis patients with Type II diabetes mellitus had H. pylori in the periodontal pocket. The prevalence of H. pylori did not differ significantly between the chronic periodontitis patients with and without type II diabetes mellitus. Meticulous scaling and root planning will reduce the prevalence of H. pylori in periodontal pockets.