Abstract Background Disturbed lipoproteins and increased oxidative stress are two of the “non-traditional” cardiovascular risk factors in chronic renal failure. There are very few prospective data of the influence of dialysis on these two factors. In the present study we investigated the effects of the initiation of both hemo- and peritoneal dialysis therapy on lipoproteins and parameters of LDL oxidation. Methods In this prospective cohort study, we assessed lipoproteins, plasma lipid peroxides and in vitro copper-induced LDL oxidation in 46 patients with end-stage renal disease prior to the start of dialysis and after 6 months of treatment with either hemodialysis ( n = 33) or peritoneal dialysis ( n = 13). Results After 6 months of treatment with hemodialysis there was an increase in total cholesterol (4.6 ± 1.1 vs. 5.0 ± 1.3 mmol/l; p < 0.05) and triglycerides (2.0 ± 0.9 vs. 2.8 ± 1.6 mmol/l; p < 0.03). In the peritoneal dialysis group the lipoproteins did not change. Regarding lipid peroxides and in vitro copper-induced LDL oxidation, also no changes were observed after 6 months of treatment in both groups. Conclusion Dyslipidemia aggravates after 6 months of hemodialysis but not after 6 months of peritoneal dialysis. During this period, no net effects on oxidative stress were demonstrated.