Background and objectives: Helicobacter pylori (H. Pylori) infection has serious consequences such as peptic ulcers and gastric cancer. Histologic identification of organisms remains the gold standard in the diagnosis of H. pylori. This meta-analysis reviewed the overall diagnostic accuracy of polymerase chain reaction (PCR) vs histology of H. pylori infection in the patients with otitis media with effusion (OME). Methods: Medline, Scopus and ISI web of science were systematically searched. Articles meeting the selection criteria were retrieved for the data collection and analysis. Diagnostic odds ratio (DOR) and symmetric summary receiver operating characteristic (sROC) of OME -associated .H. pylori infection was estimated for each study. The PCR techniques were compared to the histological tests as the gold standard in .diagnosing H. pylori infection. Results: We included eight relevant studies compromising 259 case of OME. The pooled sensitivity and specificity of PCR compared to the histological diagnosis of H. Pylori infection in patient with OME were 71% (95%CI: 61% - 80%, I2: 0.0%) and 81% (95%CI: 76% - 86%, I2: 59.9%), respectively. Pooled positive likelihood ratio (PLR) and negative likelihood ratio (NLR) for PCR were 3.61(95%CI: 2.34 – 5.59, I2: 44.5%) and 0.42 (95%CI: 0.31 – 0.57, I2: 0.1%), respectively. For DOR analysis, the pooled accuracy of PCR was 10.78 (95%CI: 5.95 – 19.53, I2: 0.0%) in diagnosing H. Pylori infection. Conclusions: This review showed statistically significant differences in the diagnostic accuracy between the PCR and histological tests. This meta-analysis also suggests a higher sensitivity and specificity of PCR-based molecular diagnostic of H. Pylori infection in OME patients compared to the histological tests.