Sixty acid-resistant Bifidobacterium isolates were recovered from human faeces and identified by genus-specific PCR and RAPD-PCR. Helicobacter pylori strains were isolated from gastric biopsies and identified by species-specific PCR. Twenty-four of the 60 Bifidobacterium isolates were considered to be different strains by RAPD-PCR. Six of the twenty-four different strains were shown to inhibit H. pylori. These antagonistic effects were related to heat-stable proteinaceous compounds, resistant to heating at 100 °C for 10 min, but sensitive to proteases. H. pylori stains showed variable resistance to therapeutic antibiotics (metronidazole and clarithromycin), while all the selected bifidobacteria showed intrinsic resistance to metronidazole. These potentially probiotic bifidobacteria were able to inhibit the growth of both antibiotic sensitive and resistant H. pylori strains. Thus, the synthesis of antimicrobial peptides could be one of the mechanisms of bifidobacteria to combat H. pylori infections.