Background and Aims: Patients undergoing upper endoscopy have often used proton pump inhibitors (PPI) and/or antibiotics (ABx) recently. Both drugs have been associated with a poorer yield of the Helicobacter pylori (H. pylori) diagnostic tests. The aim was to assess the accuracy of the polymerase chain reaction test (qPCR), histological exam (HE) and ultra-fast urease test (UFUT) for H. pylori detection in patients that recently used PPI or ABx. Methods: Prospective study recruiting 206 patients who underwent upper endoscopy and gastric biopsies. Demographics and use of PPI/ABx were obtained. Sensibility (Sn), specificity (Sp), predictive value (PV), likelihood ratio (LR) and PABAK concordance index, were calculated, considering as the gold standard the positivity of 2 out of 3 analyzed tests. A global analysis and another one based on the PPI/ABx intake were performed. Results: 48.5% of patients used PPI and 12.8% ABx within the 2 and 4 weeks prior to endoscopy, respectively. The UFUT was positive in 13.1% of patients, HE in 34% and qPCR in 35.9%. UFUT achieved lower Sn (37%) than HE (98%) and qPCR (98%) (p<0.001) overall. ABx were associated with lower Sn in HE (p=0.04) and lower Sp in qPCR (p=0.03). PPI did not associate with a significant drop in Sn and Sp. The concordance between HE and qPCR was 0.83 (95%CI: 0.73-0.89). Conclusions: Under real world conditions, the accuracy and concordance of HE and qPCR to diagnose H. pylori were excellent, but UFUT achieved unsatisfactory outcomes. The intake of ABx was associated with the worse performance, fundamentally for HE. The PPI did not reduce the tests‘ yield significantly.