Sudden cardiac death and atherosclerosis have a major impact on cardiovascular mortality in chronic kidney disease (CKD). Inflammation with elevated high-sensitive C-reactive protein (hs-CRP) is involved in both sudden cardiac death and atherosclerosis, and decreased heart rate variability (HRV) is a predictor of both sudden cardiac death and atherosclerosis. Haptoglobin (Hp) is characterised by three genotypes (1-1, 2-1, and 2-2) with different antioxidant abilities. The aim was to examine whether HRV and hs-CRP were associated with Hp genotype in CKD patients. Fifty-six patients with CKD stage 2-5 were included. Hp genotype was determined by high-performance liquid chromatography. HRV was analysed from the 24 h Holter recordings. Hs-CRP was measured using an immunoturbidimetric assay. The results show that the HRV indices SDNN and SDANN were significantly lower in the Hp 2-2 patients (P = 0.02 and 0.04, resp.). In an adjusted linear regression model, Hp 2-2 was associated with both SDNN (P = 0.005) and SDANN (P = 0.01). Hs-CRP was higher in the Hp 2-2 patients (P = 0.002). In an adjusted linear regression model, the association between Hp 2-2 and hs-CRP remained significant (P = 0.003). In conclusion, a negative association was observed between Hp 2-2 and HRV, and Hp 2-2 was positively associated with hs-CRP in CKD patients.