Background and objectives: This prospective study aimed to assess the benefits of glucose and lactose hydrogen breath tests (GHBT and Lactose HBT) on the diagnosis of respectively small intestinal bacterial overgrowth (SIBO) and lactose malabsorption in patients with irritable bowel syndrome (IBS), and also efficacy evolution of te Rifaximin in the treatment of SIBO. Materials and Methods: It was cross-sectional study with treatment and follow-up of diagnosed cases. From January 2017 to December 2018, 74 patients with IBS who visited the Gastroenterology and Hepatology Center and were diagnosed based on Rome IV criteria were studied. Patients underwent both GHBT and Lactose HBT by portable LactoFAN2. IBS symptoms severity score (IBS-SSS) was used to assess their symptoms before and after the treatment. Positive GHBT patients were given rifaximin 200 mg 3 times a day for 2 weeks followed by repeating GHBT and symptoms scoring. Results: Thirty-six patients (54%) had IBS-D, while the remaining 31 (46%) had IBS-A. glucose HBT was positive in 12(18%) patients, whereas lactose HBT was positive in 7(10%). All GHBT positive patients became negative one month after rifaximin, and their symptoms improved dramatically. Conclusion: Rifaximin is an effective therapy even at low doses for SIBO. Lactose malabsorption is prevalent mostly among diarrheal-IBS patients and those with higher calprotectin level.