The aim of the present study was to examine the association between shift work and the metabolic syndrome (MetS) using a large-scale longitudinal study design. Data were collected from a historical cohort of health checkups in the Japanese population. The baseline survey, which involved 16,952 inhabitants of the Minami Saku area of the Nagano Prefecture, was started in 1978. A nested case-control study was conducted between 1987 and 1990. This analysis was restricted to 6,712 men and women (age range 25-59 years). A conditional logistic regression model was used to estimate the risk of MetS associated with shift work. Compared with the day workers, shift workers had a significantly higher risk of MetS (odds ratio 1.87; 95% CI, 1.13-3.08). Our results demonstrate that shift work was strongly associated with MetS. The study suggests appropriate dietary habits as a basis for managing the MetS risk of shift workers.