Background and Aims In contrast to guideline recommendations, endoscopic testing for Helicobacter pylori is frequently performed under Helicobacter pylori suppressive conditions, e.g., intake of proton-pump inhibitors (PPI), preceded antibiotic treatment, or recent gastrointestinal bleeding. Our study's aim was to retest patients with—under suppressive conditions—negative test results. This was carried out in order to examine the rate of false negative tests previously gathered under suppressive conditions. Methods The trial was conducted in a large patient collective in a university hospital. Every elective esophagogastroduodenoscopy from in- and outpatients was included. Prior to endoscopy, suppressive conditions were collected via standardized questionnaire. If Helicobacter pylori testing was indicated, both helicobacter urease test and histology were performed in analogy to the Sydney classification. In case of a negative result under suppressive conditions, the patient was reinvited after, if possible, withdrawal of suppressive condition in order to perform a urea breath test (UBT). Results 1,216 patients were included (median 59 years, 72.0% inpatients, 28.0% outpatients). Overall, 60.6% (737) were under Helicobacter pylori suppressive conditions. The main suppressive condition was intake of PPIs (54.5%). In 53.7% (653) of all included cases, Helicobacter pylori testing was performed. Of those, 14.1% (92) had a positive test, and 85.9% (561) were negative. Out of the patients with negative result, 50.8% (285) were tested under suppressive conditions and consequently invited for retesting via UBT. In 20.4% (45), suppressive conditions could not be ceased. In 22.8% (65), retesting was conducted. Of those, 98.5% (64) congruently presented a negative result again, and only 1.5% (1) was positive for Helicobacter pylori. Conclusion Many patients undergoing esophagogastroduodenoscopy in everyday clinical practice are tested for Helicobacter pylori under suppressive conditions leading to a potentially higher risk of false negative results. However, our research shows that this issue might be overestimated.