Several health-promoting effects of kefir have been suggested, however, there is limited evidence for its potential effect on gut microbiota in metabolic syndrome This study aimed to investigate the effects of regular kefir consumption on gut microbiota composition, and their relation with the components of metabolic syndrome. In a parallel-group, randomized, controlled clinical trial setting, patients with metabolic syndrome were randomized to receive 180 mL/day kefir ( = 12) or unfermented milk ( = 10) for 12 weeks. Anthropometrical measurements, blood samples, blood pressure measurements, and fecal samples were taken at the beginning and end of the study. Fasting insulin, HOMA-IR, TNF-α, IFN-γ, and systolic and diastolic blood pressure showed a significant decrease by the intervention of kefir ( ≤ 0.05, for each). However, no significant difference was obtained between the kefir and unfermented milk groups ( > 0.05 for each). Gut microbiota analysis showed that regular kefir consumption resulted in a significant increase only in the relative abundance of ( = 0.023). No significant change in the relative abundance of by kefir consumption was obtained. Furthermore, the changes in the relative abundance of sub-phylum bacterial populations did not differ significantly between the groups ( > 0.05, for each). Kefir supplementation had favorable effects on some of the metabolic syndrome parameters, however, further investigation is needed to understand its effect on gut microbiota composition.