<p>Antibiotic resistance and virulence factor of <i>Helicobacter pylori</i> pose formidable challenge towards eradication of this pathogen. Heterogeneity of <i>H. pylori cag</i>PAI is essential in the emergence of antibiotic resistance. The objective of this study was to investigate the correlation between antibiotic resistance and <i>cag</i>PAI variability among <i>H. pylori</i> strains in multiethnic Malaysian patients. <i>H. pylori</i> antibiotic susceptibility profile to six antibiotic classes was determined using E-test and the presence of each <i>cag</i>PAI gene was determined using polymerase chain reaction (PCR). The highest resistance was observed against metronidazole (58.6%, 34/58), followed by clarithromycin (36.2%, 21/58), and levofloxacin (25.9%, 15/58); all strains were susceptible to amoxicillin, tetracycline and rifampicin. Clarithromycin-resistance in <i>H. pylori</i> was significantly higher among elderly patients (&gt; 50&#xa0;years old) (<i>P</i> = 0.040). Isolates harboring complete <i>cag</i>T4SS genes exhibited significantly higher resistance to antibiotic treatments, primarily towards a single antibiotic (<i>P</i> = 0.043). Resistance to a single antibiotic was significantly higher in East Asian strains (<i>P</i> = 0.027), of which majority of the infected patients were Chinese. Among the resistant isolates, 20.9% (9/43) exhibited multi-drug resistance (MDR), demonstrating resistance to metronidazole, clarithromycin, and levofloxacin concurrently. Female patients were notably at higher risk of being infected with MDR-<i>H. pylori</i> (<i>P</i> = 0.022) than males. Our findings offer insights into the association between variability of <i>cag</i>PAI and antibiotic resistance in <i>H. pylori</i>, of which further research is warranted to elucidate the mechanisms underlying <i>cag</i>PAI heterogeneity and antibiotic resistance in <i>H. pylori</i> for effective therapeutic strategies.</p>