This study was aimed at procuring directly and identifying the bacteria which had been found in paraffin-embedded liver tissues of hepatocellular carcinoma (HCC) patients. In our previous studies, Helicobacter spp. had been detected by polymerase chain reaction (PCR) and observed by histology in the liver tissues of HCC patients but had never been cultured successfully. To obtain and identify the uncultured bacteria, laser microdissection and pressure catapulting (LMPC) techniques were applied. Following microdissection from the liver tissue sections, these bacteria were examined by PCR using Helicobacter genus-specific 16S rRNA primers and sequence analysis. Amplified products of 16S rRNA were positive in all six microdissected samples with bacteria, and showed 99%-100% similarity with Helicobacter pylori by sequence analysis. Another H. pylori-specific 26 kDa gene (encoding one 26 kDa protein as H. pylori-specific antigen) was also tested by PCR. Four of six samples were positive. Therefore, Helicobacter spp. detected by PCR in the liver tissues of HCC patients in our previous studies are actually the bacteria observed by histology and identified as H. pylori by further sequence analysis. The laser-assisted microdissection technique can be extensively applied for identification of bacteria in tissue samples in bacteriology research.