Context Functional dyspepsia is a condition in which symptoms are not related to organic underlying disease; its patho genesis is not well known. The small intestinal bacterial overgrowth (SIBO) is characterized by the increase in the number and/or type of colonic bacteria in the upper gastrointestinal tract. The hypothesis of SIBO being associated to functional dyspepsia must be considered, since the impaired motility of the gastrointestinal tract is one of the main etiologic factors involved on both pathologies. Objective To determine if there is SIBO in patients with functional dyspepsia. Methods Case control study, evaluating 34 patients: 23 functional dyspeptic and 11 non dyspeptic (control group). Questionnaire applied based on Rome III criteria. The patients un derwent H 2 lactulose breath test, considered positive when: H 2 peak exceeding 20 ppm, in relation to fasting, or two peaks exceeding 10 ppm sustained until 60 minutes. Results Of the 23 dyspeptic patients, 13 (56.5%) obtained positive results for SIBO trough the H 2 lactulose breath test. On control group, SIBO was not observed. The association between the dyspeptic group and the control group regarding SIBO was statistically significant, with P = 0.0052. In the group of dyspeptic patients, 12 (52.2%) were using proton pump inhibitor; of these 9 (75%) were positive for SIBO. In the control group, none of the 11 patients used proton pump inhibitors and SIBO was not observed. The association of the dyspeptic group using proton pump inhibitor that were positive for SIBO and the control group was statistically significant, with P = 0.0011. Conclusion It was found that, patients with functional dyspepsia presented SIBO, when they underwent to H2 lactulose breath test, compared to the non dyspeptic. In addition, it was observed a higher prevalence of SIBO in dyspeptic patients that were using proton pump inhibitors, compared to control group.