Postoperative complications in cardiovascular surgery remain an important unresolved problem, in particular in patients with aortic aneurysm. The role of the altered microbiota in such patients is of great interest. The aim of this pilot study was to determine whether the development of postoperative complications in patients with aortic aneurysm is related with initial or acquired disorders of microbiota metabolism by monitoring the level of some aromatic microbial metabolites (AMMs) circulating in the blood before the surgery and in the early postoperative period. The study comprised patients with aortic aneurysm (n= 79), including patients without complications (n= 36) and patients with all types of complications (n= 43). The serum samples from the patients were collected before and 6 h after the end of the surgery. The most significant results were obtained for the sum of three sepsis-associated AMMs. This level was higher before the surgery in comparison with that of healthy volunteers (n= 48),p< 0.001, and it was also higher in the early postoperative period in patients with all types of complications compared to those without complications,p= 0.001; the area under the ROC curve, the cut-off value, and the odds ratio were 0.7; 2.9 µmol/L, and 5.5, respectively. Impaired microbiota metabolism is important in the development of complications after complex reconstructive aortic surgery, which is the basis for the search for a new prevention strategy.