There has been conflicting results regarding the presence of H. pylori in tonsillar tissue. Our objective was to analyze for the presence of H. pylori in tonsillar tissue in patients undergoing tonsillectomy for chronic recurrent tonsillitis using rapid urease test in a Tertiary care academic medical center in a sub Saharan hospital. A prospective cross-sectional analysis of 39 consecutive cases of patients undergoing tonsillectomy secondary to chronic recurrent tonsilitis was done. Rapid urease test was conducted on each tonsillectomy tissue and results were determined using color change at specific time intervals within 24 h. Average age of the patients was 4.3 years. Among the 39 tonsillar tissues analysed using rapid urease test, H. pylori was present in 30.5 % of the samples. Colonisation by H. pylori of the palatine tonsils is a new frontier with conflicting results depending on the accuracy of the test method used and population studied. More studies need to be performed to ascertain the different rates of colonisation based on geographical regions.