The relationship between methanogenic flora and hydrogen (H(2)) production is considered to be a possible confounding factor in the interpretation of hydrogen breath tests (H(2)BT). Therefore, the present study was conducted prospectively and included 154 IBS patients (fulfilling Rome II criteria) and 286 age-and-sex-matched apparently healthy controls. Each subject underwent H(2)BT after overnight fasting using 25 g lactose. Methane and H(2) were measured using an SC Microlyser from Quintron, USA, at baseline and every 30 min for a total of 4 h. Subjects with fasting methane concentration <10 ppm were labeled as low methane producers (LMP) and >10 ppm as predominant methane producers (PMP). A rise >20 ppm over base line in hydrogen concentration was taken as +ve hydrogen breath test. IBS and control groups included 66.78% and 67.53% males, respectively. Mean age in the two groups were 48.52 +/- 30.54 years (range 15-68 years) and 45.67 +/- 30.54 years (range 15-78 years), respectively. Hydrogen breath test was +ve in 77/154 (50%) IBS patients and in 142/286 (49.65%) in controls (P > 0.05). It was also observed that the hydrogen breath test was -ve due to PMP in 5/77 (6.49%) of IBS patients and in 29/154 (20.14%) in controls. PMP affected lactose hydrogen breath tests in 6.49-20.14% subjects. This effect is more apparent in apparently healthy subjects as compared to patients with IBS.