The antibacterial activity of polyoxometalates (PMs) against Helicobacter pylori was investigated based on determinations of minimum inhibitory concentration (MIC) and fractional inhibitory concentration (FIC), time-killing of the bacteria, bacterial morphology and PM-uptake into the bacteria cell. The result of MIC values revealed that, of 13 PMs used in this study, highly negative-charged polyoxotungstates, such as K27[KAs4W40O140] and K18[KSb9W21O86], and Keggin-structural polyoxotungstates exhibited a potent antibacterial activity with the MIC values of less than 256 microg/ml. The former was the most active, and superior to metronidazole (MTZ) against MTZ-susceptible and resistant strains and also to clarithromycin (CLR) against CLR-resistant strains. In contrast, most of polyoxomolybdates showed little antibacterial activity with the MIC values of more than 256 microg/ml. The result of FIC index values indicated that the antibacterial polyoxotungstates had partially synergistic effect in combination with MTZ and CLR but indifferent effect in combination with amoxicillin (AMX). From the results of the time-killing and scanning electron microscope images, K27[KAs4W40O140] and K18[KSb9W21O86] proved the concentration-dependent bactericidal activity with the morphological change from bacillary form to coccoid form, while Keggin-structural K5[SiV(V)W11O40] showed the bacteriostatic activity with small change of morphology to coccoid form. The fluorescent X-ray analysis demonstrated that these polyoxotungstates were taken into the bacteria cell. It is pointed out that the Keggin-structure and/or high negativity polyoxotungstates are an important factor for the antibacterial activity against H. pylori.