BACKGROUND : We reported in a previous study that photodynamic therapy (PDT) of Helicobacter pylori(H. pylori) could potentiate bactericidal effect by adding chitosan. As a next step, we compared the bactericidal effects of low molecular weight (LMW) combined with Photodynamic Therapy to high molecular weight (HMW) chitosan. METHODS : To perform PDT to kill H. pylori, we used endoscopic light as light source, methylene blue (MB) as a photosensitizer and chitosan (310-375, 50-190 kDa). We evaluated bacterial removal rate and its membrane damage by ethidium bromide monoazide PCR method (EMA q-PCR). 8-oxo-2'-dexoyguanosine by ELISA was measured for oxidative stress. RESULTS : At a chitosan concentration of ≤0.05%, the killing effect did not differ between the two molecular weights, and 100% bacterial removal rate was observed at a light energy ≥ 6.23 mJ/cm2 powers under 0.02% MB. After 15 min irradiation, LMW chitosan with high concentration of MB (0.004%) showed highest killing effects, which were consistent with the results of EMA q-PCR but not with the level of 8-OHdG. Bactericidal effects of LMW chitosan plus PDT using 0.002 and 0.004% MB for 15 min irradiation were significantly higher than those using HMW chitosan plus PDT. CONCLUSIONS : We found that PDT using methylene blue with LMW chitosan to kill H. pylori exerted greater bactericidal effects through bacterial membrane damage than PDT with HMW chitosan. These results suggest that it would be better to choose LMW chitosan to enhance the effect of PDT for clinical application, even at a very low concentration of PS.