Background: Hydrogen breath tests are widely used in clinical practice. For a correct evaluation of data, low basal H2 excretion is required, thus, 12-hour fasting is usually prescribed. An additional reduction in the intake of complex carbohydrates in the preceding 24 h is suggested in some centers. The issue, however, has never been directly investigated. Aim: The aim of the present study was to analyze the effect of the pretest diet on the basal H2 excretion and the number of subjects excluded from the test due to high basal H2 excretion. Methods: Two cohorts of 500 consecutive patients undergoing a lactose tolerance test in the years 1997–1998 (when 12-hour fasting was required) and in 2007–2008 (when a low-carbohydrate diet in the preceding 24 h was also prescribed) were retrospectively reviewed. Results: The mean basal H2 excretion was significantly lower (p < 0.0001) in the low-carbohydrate diet group (2.46 ± 6.8 vs. 4.73 ± 3.3 ppm). In 1997–1998, 46/500 patients (9.2%) were excluded from the test due to basal H2 values as compared to 7/500 (1.4%) in the period 2007–2008. Discussion: To the best of our knowledge, ours is the first study to provide objective data on the advantage offered by reducing the intake of complex carbohydrates before H2 breath tests.