Different Helicobacter pylori genes may be well conserved within different ethnic groups and could give rise to different clinical outcomes. In this study, we demonstrated a low prevalence of H. pylori infection (19.2%) which is in concordance with the current trend demostrated locally and abroad. The Indians had the highest prevalence of H. pylori infection among other ethnic groups (Malays= 8.6 %, Chinese= 24.3 %, Indians= 33.9%). cagM and cagT were the most predominant genes found (63.4% for each), followed by cagA (62.2 %), cagE (48.2%), cag6-7 (46.3%), cag10 (42.1%), cag13 (4.9%) and IS605 (3.7%). No significant association was found between H. pylori infection and H. pylori genes with ethnic groups or clinical outcomes. Indians who had a combination of cagA/ E/M genes of H. pylori were likely to be associated with 21-time of having non-ulcer dyspepsia (NUD) than peptic ulcer disease (PUD). Therefore, these genes may serve as useful markers in predicting the clinical presentation of a H. pylori infection among Indians in our studied population. Hence, this preliminary data might explain why Indians have a low prevalence of gastric cancer and peptic ulcer disease despite having persistently high prevalence of H. pylori infection for many decades (“Indian enigma”) in Malaysian patients.