Intestinal disorders and vascular calcification (VC) are often associated with chronic kidney disease (CKD). While gut barrier alterations have been reported in CKD (abnormal intestinal permeability, bacterial overgrowth and inflammation), it is not clear if vascular calcification influences such alterations. Bidirectional relationships between VC and gut dysfunction could be mediated by increased inflammation and uremic toxin generation. We used the SNx-VC model of uremic vascular calcification (rats undergoing subtotal 5/6th nephrectomy and fed a pro-calcifying high-phosphate and vitamin D diet) to investigate gut alterations in vivo. We confirmed the presence of CKD and VC (von Kossa), and observed increased gut-origin uremic toxin, indoxyl sulfate (IS), in SNx-VC animals compared to controls. In SNx-VC, we observed a decreased mucus production (Alcian blue, Mucin 2 staining) in colon and ileum that correlated with calcification severity. There was no change in inflammation markers or tight junction proteins expression. We assessed intestinal levels in the NOD‐like receptor family pyrin domain containing 6 (NLRP6) protein, known to regulate mucus secretion, and found no change in colon or ileum. NLRP6 mRNA was however decreased in SNx-VC in colon, along with other mRNA (Ly96, Sod1), while Tlr2 was increased. Our observations of low mucus, low Nlrp6 mRNA, and high IS in SNx-VC confirm a link between gut barrier alterations and uremic VC. This suggests that alterations in the mucus layer could favour the generation of gut-origin uremic toxins and promote VC in CKD.