Objective: Our study investigated the correlations of individual chronotype, social jetlag (SJL), and sleep duration with levels of atherogenic lipids. Methods: This cross-sectional study included 1,984 participants who visited the health checkup centers of two tertiary medical institutions from July 2016 to December 2016. Chronotype was assessed by the Morningness−Eveningness Questionnaire (MEQ), and sleep duration and SJL were assessed by a self-reported questionnaire. Simple and partial Pearson's correlation analyses were used to investigate the relationship between sleep parameters and lipid profiles. Multiple stepwise and enter method regression analyses were used to find independent relationships between MEQ score and atherogenic index of plasma (AIP). Results: Participants' MEQ scores were significantly correlated with triglyceride levels (r=-0.088, p<0.01), total cholesterol/high-density lipoprotein (TC/HDL; r=-0.059, p<0.05), and AIP (r=-0.089, p<0.01). Their SJL scores were positively related with TC (r=0.055, p<0.05), while sleep duration was negatively related with HDL-cholesterol (r=-0.053, p<0.01). Partial Pearson's correlation analysis showed that MEQ score was more strongly associated with AIP (r=-0.089) than with SJL and sleep duration (p=0.011 and p=0.031), respectively. A significant association between MEQ score and AIP was found by multiple linear regression analyses after adjusting for age, sex, body mass index, mean arterial pressure, glucose level, white blood cell count, smoking status, physical activity, alcohol consumption, and dyslipidemia medication (β=-0.002, p=0.009). Conclusion: Late chronotype is independently and negatively associated with AIP after adjusting for possible confounders, suggesting these individuals are at increased risk for cardiovascular disease and may benefit from chronotherapy to limit its incidence in this population.