The present study examined the associations between polymorphisms in genes involved in lipid metabolism and the risk of CKD in the Japanese population, and identified a total of four SNPs (two in APOA5 (T − 1131C [rs662799] and T1259C [rs2266788]), TOMM40 A/G (rs157580), and CETP TaqIB (G > A) (rs708272)) that were significantly associated with CKD risk. This evidence concerns the gene CETP and chronic kidney disease.