The aim of this research was to study the association between the gut microbiota composition and arterial wall properties. The study included 92 participants, men and women aged 25–76 years old without clinical manifestation of chronic diseases but with the possible presence of cardiovascular risk factors. Carbohydrate metabolism examination, duplex scanning of the carotid arteries with the measurement of the intima-media thickness (IMT), the carotid-femoral pulse wave velocity (PWV) measurement, and 16S rRNA (V3[sbnd]V4 regions) sequencing of the gut microbiota were performed in all participants. Higher Serratia abundance was associated with the increased IMT and CRP levels. Blautia representation was associated with IMT. Higher Bacteroides representation was associated with higher pulse wave velocity in non-diabetic subjects. Although this study had some limitations, we have demonstrated that the composition of the gut microbiota was associated both with atherosclerotic and arterial stiffness markers. © 2017 Association for Research into Arterial Structure and Physiology