The relation between shift work and a large variety of cardiometabolic risk factors is unclear. Also, the role of chronotype is understudied. We examined relations between shift work and cardiometabolic risk factors, and explored these relations in different chronotypes. Cardiometabolic risk factors (anthropometry, blood pressure, lipids, diabetes, γ-glutamyltransferase, C-reactive protein, uric acid and estimated glomerular filtration rate) were assessed among 1334 adults in 1987-91, with repeated measurements every 5 years. Using shift work history data collected in 2013-15, we identified shift work status 1 year prior to all six waves. Linear mixed models and logistic generalized estimating equations were used to estimate the longitudinal relations between shift work and risk factors 1 year later. Shift work was not significantly related with cardiometabolic risk factors (P ≥ 0.05), except for overweight/body mass index. Shift workers had more often overweight (OR: 1.44, 95% CI 1.06-1.95) and a higher body mass index (BMI) (β: 0.56 kg m -2 , 95% CI 0.10-1.03) than day workers. A significant difference in BMI between day and shift workers was observed among evening chronotypes (β: 0.97 kg m -2 , 95% CI 0.21-1.73), but not among morning chronotypes (β: 0.04 kg m -2 , 95% CI -0.85 to 0.93). No differences by frequency of night shifts and duration of shift work were observed. Shift workers did not have an increased risk of cardiometabolic risk factors compared with day workers, but, in particular shift working evening chronotypes, had an increased risk of overweight. More research is needed to verify our results, and establish whether tailored interventions by chronotype are wanted.