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Background: Papillary thyroid cancer (PTC) is the most common type of thyroid cancer and the incidence of PTC has continued to increase over the past decades. Many studies have shown that obesity is an independent risk factor for PTC and obese PTC patients tend to have a relative larger tumor size and higher grade of tumor stage. Obesity is associated with disordered lipid metabolism and the relationship between serum lipids and PTC remains unclear. Therefore, this study aimed to investigate the association between serum lipid level and PTC. Methods: We retrospectively analyzed 1018 PTC patients diagnosed and treated in our hospital, all these cases were first diagnosed with PTC and had complete clinical information including ultrasound reports before surgery, serum lipid (CHOL, TG, HDL-c, LDL-c, Apo-A1, Apo-B, Apo-E) results, surgical records and pathological reports. Results: None of these lipid markers were associated with tumor size in the whole cohort and in the female group. In the male group, on crude analysis, Apo-A1 showed a marginally association with tumor size, [OR = 0.158 (0.021–1.777)], p = 0.072. After adjusting for age and multifocality, Apo-A1 showed a significant association with tumor size [OR = 0.126 (0.016–0.974)], p = 0.047. This association become more apparent in a young male subgroup, [OR = 0.051 (0.005–0.497)], p = 0.009. CHOL, TG, HDL-c, LDL-c, Apo-B, Apo-E did not show significant association with tumor size. As for LNM, neither in the male group nor in the female group were found to be associated with any serum lipid biomarkers. Conclusion: As PTC incidences continues to increase, our findings demonstrated a negatively association between PTC and apoA-1 in male PTC patients, which may contribute to further investigation concerning diagnosing and preventing this most common type of thyroid cancer. [ABSTRACT FROM AUTHOR]