Background Some studies have shown that a high level of bilirubin is a protective factor against the metabolic syndrome (MS), while a high level of transaminase is a risk factor for the MS. However, the results are inconsistent, and there are few cohort studies.Methods Using an ambispective cohort study, 565 Kazakhs from Xinjiang, China were selected as the study subjects. The serum bilirubin and transaminase levels of the subjects were divided into quartiles, and their relationships with MS and its components were analyzed. The definition of metabolic syndrome was based on the Joint Interim Statement (JIS) diagnostic criteria.Results The average follow-up time for the subjects was 5.72 years. 204 subjects had MS, the cumulative incidence was 36.11%, and the incidence density was 63.10/1000 person-years. Multivariate Cox regression analysis showed that the levels of total bilirubin (TBIL) and indirect bilirubin (IBIL) were negatively correlated with the occurrence of MS. Compared to the lowest quartile level (Q1), the hazard ratios of MS for levels of TBIL at the Q2-Q4 quartile were: 0.408 (0.266-0.626), 0.374 (0.244-0.572), and 0.328 (0.216-0.500) while IBIL at Q2-Q4 level showed an MS hazard ratio of 0.572 (0.374-0.875), 0.432 (0.283-0.659), 0.434 (0.289-0.653), all at a 95% confidence level. In addition, TBIL and IBIL levels were negatively correlated with increased blood pressure, waist circumference, and triglyceride levels, and their highest TBIL quartile risk (Q4) was 0.479, 0.484, and 0.498 times higher than the lowest quartile (Q1).Conclusion Serum TBIL and IBIL levels were negatively correlated with MS and its components (blood pressure, waist circumference and triglycerides).