There is inconsistent evidence about the association between Helicobacter pylori (H.pylori) and dental diseases with possible effect of environmental factors. The aims of the study were to assess (1) the association between gastric and oral H.pylori colonization and (2) the association between oral colonization of H.pylori and dental diseases. A cross-sectional study was conducted in King Fahad University hospital in Khobar, Eastern Saudi Arabia in 2017. Patients admitted to the Endoscopy Unit were recruited and clinically examined for plaque, decayed teeth (D), filled teeth (F), missing teeth (M), periodontal pocket depth (PPD), attachment loss (AL), and gingival bleeding in addition to assessing their age, gender, education, tooth brushing, flossing, and tobacco use with a questionnaire. Pooled dental plaque samples were collected and analyzed using nested polymerase chain reaction PCR to detect oral H.pylori. Gastroscopy was used to extract biopsies to assess gastritis and the presence of gastric H.pylori using Giemsa stain. Regression analysis was used to assess differences between patients with and without gastritis, oral H. pylori and gastric H. pylori in the percentage of sites with gingival bleeding, PPD, CAL, D, M, and F with adjustment for confounders. One hundred twenty patients were included. Most of them brushed daily (82.6%) and had university education (45.7%). Of these, 34.2% had gastric H.pylori and 5% had oral H.pylori. No significant association was observed between the percentage of sites with gingival bleeding, mean PPD, AL, F, and either gastritis, the presence of oral or gastric H.pylori. Patients with gastritis had significantly higher number of D and M than patients without gastritis (P= 0.03). In this study, the presence of gastric and oral H.pylori in patients with good oral hygiene and moderate socioeconomic status is not significantly associated with periodontal diseases. Patients with gastritis tend to have a higher number of decayed and missing teeth.