Small noncoding RNAs (sRNAs) are a group of regulatory RNA molecules normally without a protein-coding function. In recent years, the importance of sRNAs as mediators of gene expression in bacteria has begun to be recognized. More than 70 sRNAs have been known in Escherichia coli. However, little is known about sRNAs in Helicobacter pylori, a human pathogen associated with gastric diseases. Here, we systematically identified sRNAs in the H. pylori genome by a computational approach based on gene location, sequence conservation, promoter and terminator search, and secondary structure. Among a total of six candidate sRNAs initially predicted, two novel sRNAs (IG-443 and IG-524) were confirmed by Northern blot and reverse transcription-polymerase chain reaction (RT-PCR). Virtually, they were a class of natural antisense transcripts, which were complementary to partial sequences of the following genes: flagellar motor switch gene (fliM) and fumarase (fumC). Taken together, the results indicate that there exist novel sRNAs in H. pylori and these RNAs might play a potential role in regulating gene expression.