<i>Background:</i> Dyslipidemia is a common complication of chronic kidney disease. Lipoprotein lipase (LPL) 1595 C/G and hepatic lipase (HL) –480 C/T single nucleotide polymorphisms (SNPs) influence lipid profile and predisposition for cardiovascular disease in the general population. The present study was undertaken to clarify the impact of the two polymorphisms on lipid parameters and cardiovascular risk in incident dialysis patients. <i>Methods:</i> LPL 1595 C/G and HL –480 C/T SNPs were evaluated in 293 chronic kidney disease patients close to dialysis initiation. Associations with lipid parameters, presence of cardiovascular disease, and survival were assessed. <i>Results:</i> LPL 1595 C/G SNP was associated with significantly lower triglyceride levels [1.55 (1.00–2.20) vs. 1.90 (1.40–2.48) m<i>M</i>; p < 0.01], while HL –480 C/T polymorphism was associated with increased high density lipoprotein cholesterol concentration [1.30 (1.00–1.60) vs. 1.10 (0.90–1.40) m<i>M</i>; p < 0.05]. Neither of the polymorphisms showed any relationship with patient survival. <i>Conclusions:</i> LPL 1595 C/G and HL –480 C/T polymorphisms affect lipid profile in incident dialysis patients.