Combination antibiotic therapy for Helicobacter pylori has now become the standard means of treating peptic ulcer diseases. Clarithromycin is a newly adopted antibiotic for H. pylori eradication. However, resistance to clarithromycin reduces the efficacy of clarithromycin-containing regimens. We explored mechanisms of clarithromycin resistance by evaluating H. pylori for macrolide resistance mechanisms reported in H. pylori and other bacteria. Degenerate polymerase chain reaction analysis of the H. pylori genome failed to yield products homologous to methylase, a drug inactivation enzyme, or efflux pumps. Clarithromycin selection in Escherichia coliNM522, transformed with an expression library that was constructed with genomic DNA from a clarithromycin-resistant strain of H. pylori, revealed six clones that conferred clarithromycin resistance consistently after retransformation. Southern hybridization and DNA sequencing revealed that four of the six clones contained the same locus. Comparison of DNA and amino acid sequences showed that the 1.3-kb DNA fragment had significant homology to the 3-oxoadipate CoA-transferase subunit A (yxjD) and subunit B (yxjE) of Bacillus subtilis. However, the clarithromycin inactivation assay and knockout mutation analysis showed that the gene increased clarithromycin resistance in E. coli, but not in H. pylori. In contrast, sequencing of the 23S rRNA gene in six clarithromycin-resistant H. pylori clinical isolates revealed an A to G transitional mutation at position 2515 of the 23S rRNA gene in all isolates. Natural transformation with the 23S rRNA gene from resistant strains conferred clarithromycin resistance in clarithromycin-sensitive strains. We conclude that the 23S rRNA mutation is sufficient to confer clarithromycin resistance and that it is the major mechanism of clarithromycin resistance in H. pylori.