Background: Helicobacter pylori (H.pylori) infection is highly prevalent worldwide, with an overall infection rate of 50% of the total population. Effective and accurate eradication treatment for H.pylori is considered one of the most important preventative measures against gastric cancer. However, the increasing prevalence of clarithromycin-resistant H. pylori strains has significantly compromised the success rates of standard eradication regimens. In recent years, many countries have adopted molecular diagnostic methods to detect H.pylori infection and assess clarithromycin resistance. These approaches, which are often non-invasive, enhance both diagnostic accuracy and the ability to tailor treatment strategies. Although numerous studies have investigated methods for detecting H. pylori and clarithromycin resistance using gastric tissue specimens, relatively few have focused on the clinical application of stool-based diagnostics, despite their potential advantages in non-invasive testing. Aim: To detect H.pylori infection and clarithromycin resistance using molecular biological methods from both gastric tissue and stool samples, and to comparatively evaluate the diagnostic outcomes. Materials and Methods: The hospital-based cross-sectional study was conducted at the Gastroenterology department of the Mongolia-Japan Hospital. A total of 125 dyspeptic patients aged 18-80 years were enrolled. Eligibility criteria required the H.pylori infection to be confirmed by at least two diagnostic methods. Each participant underwent both invasive (histological examination, gastric biopsy-based real-time PCR) and non-invasive (urea breath test, stool antigen test, stool-based real-time PCR) methods. Gastric biopsies and stool samples were analyzed by real-time PCR to detect H.pylori and identify clarithromycin resistance-associated 23S rRNA point mutations (A2143G, A2142G, A2142C) Results: Among the study participants, 60.0% (n=75) were female and 40.0% (n=50) were male, with a mean age of 39±1 years. Comparative evaluation of the diagnostic methods for H.pylori infection demonstrated that the stool antigen test, performed in 104 individuals, yielded positive results in 91 cases (87.5%), whereas the urea breath test, performed in 51 individuals, was positive in 45 cases (88.2%). Using real-time polymerase chain reaction (PCR), H.pylori was detected in 76 of 101 stool samples (75.2%) collected in ENAT transport medium, and in 43 of 87 raw stool samples (49.4%). The estimated diagnostic sensitivities were 94% for the urea breath test, 91% for the stool antigen test, 78% for real-time PCR using ENAT-preserved stool, and 49% for real-time PCR using raw stool specimens. Clarithromycin resistance was found in 36 participants (28.8%), while 89 participants (71.2%) carried H.pylori strains susceptible to clarithromycin. Clarithromycin resistance was detected in 27.6% of stool samples and 30.5% of gastric biopsy specimens. Among the clarithromycin-resistant isolates identified from gastric tissue, 35 cases (97.2%) carried the A2143G point mutation, while the A2142G mutation was detected in only 1 case (2.8%). All resistant cases detected from stool samples carried the A2143G mutation, whereas the A2142G mutation was not observed. Conclusion Real-time PCR demonstrated high efficacy for the detection of H.pylori infection and clarithromycin resistance in gastric biopsy specimens. While the sensitivity of stool-based real-time PCR was comparatively lower, detection rates improved with the use of ENAT transport medium. These findings highlight the potential of stool-based real-time PCR as a non-invasive diagnostic tool; however, further investigations are warranted to optimize assay performance through rigorous standardization and refinement of sample processing protocols for the accurate detection of clarithromycin-resistant H.pylori.