H. pylori is a gram-negative bacterium associated with gastric inflammation and peptic ulcer and considered a risk factor for gastric cancer in its natural habitat. However, the energy metabolism of H. pylori in the stomach remains to be clarified. H. pylori shows rather high respiratory activity with L-proline and significantly large amounts of L-proline are present in the gastric juice from H. pylori infected patients. We constructed a disrupted mutant of the put A gene, which encodes the proline utilization A (Put A) flavin-linked enzyme, in order to examine the role of put A in the gastric colonization of H. pylori. The put A disrupted mutant, ΔputA, was constructed by inserting a chloramphenicol resistant gene into put A. Δput A did not show respiratory activity using L-proline and could not incorporate L-proline into cells. Δput A also did not show motility in response to amino acids and did not display the swarming activity observed with the wild-type. Δput A had lost its ability to colonize the stomach of nude mice, an ability possessed by the wild-type. These findings indicate that put A may play an important role in H. pylori colonization on the gastric mucus layer.