The serum levels of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) were measured in a middle-aged Korean population and investigated associations with age, gender, body mass index (BMI), metabolic syndrome (MS), type 2 diabetes mellitus (T2DM), and dietary habits. The median concentrations of 22 OCPs and 34 PCBs in the serum samples were 483 and 216 ng g lipid, respectively. The most abundant compound was p,p'-DDE, followed by PCB 153, β-HCH, PCB 118, and PCB 180. The results of multiple linear regression and other statistical analyses revealed that serum OCP and PCB levels were higher in women and were positively correlated with age. BMI was positively associated with serum OCP and PCB levels, reflecting the influence of food intake and the preserving effect of body fat. MS and T2DM were significantly associated with serum OCP and PCB levels. The intake of animal foods had positive associations with serum OCP and PCB levels, whereas the intake of phytogenic foods showed negative associations, presumably because of contamination levels in food items and food matrices that governs absorption and excretion of OCPs and PCBs in the body. The relationship between dietary habits and serum OCP and PCB levels were different in participants with MS compared to healthy participants, suggesting MS may alter the influence of food intake on serum OCP and PCB levels.