Aims: The aim of this study was to investigate the relationship between longitudinal change in total cholesterol as a main cardiovascular disease risk factor and shift work, controlling for the effect of the weight at baseline of recruitment. Materials and Methods: This retrospective cohort study consists of 674 employees of Iranian Corporation Polyacril from 1992 to 2009. Stratified analysis of the relationship between shift work and cholesterol based on weight status at baseline of recruitment controlled for the effect of confounders including age, body mass index, pre-employment cholesterol, glucose, triglyceride, urea, work types, education, and marital status. A linear mixed model used for analyzing the data. Estimation of parameters has done by Bayesian approaches using Winbugs statistical software. Bayesian confidence interval (CI) was used for testing regression coefficients. Results: Average age mean at employment was 25 years (standard deviation [SD] =3.3); the average number of measurement for each individual was 3.7 times (SD = 0.6). In this model, relationship between shift work and cholesterol changes controlled for confounding factors was significant in whom overweight was at baseline (beta = 2.25, P < 0.001, 95% CI: 0.67-3.88) but was not significant for whom overweight was at baseline of employment. Conclusions : The rate of cholesterol changes was higher for normal weight shift workers compared with workers who were overweight at baseline of recruitment.