Microscopic haematuria is proposed as a prognostic factor for renal outcomes in patients with glomerulonephritis. However, the role of haematuria in patients with advanced chronic kidney disease (CKD) or heavy proteinuria has not been investigated. We divided 1799 patients with stage 3-5 nondiabetic CKD into 3 groups according to the results from 3 urinalyses: no haematuria (0-2 red blood cells [RBCs]/hpf ≥2 times), mild haematuria (2-5 RBCs/hpf ≥2 times) and moderate haematuria (≥5-10 RBCs/hpf ≥2 times). The estimated glomerular filtration rate was 25.4 mL/min/1.73 m(2), with a urine protein-to-creatinine ratio (UPCR) of 881 mg/g. The hazard ratios (HRs) of mild and moderate haematuria for end-stage renal disease (ESRD) were 1.28 (95% confidence interval [CI]: 1.05-1.56, P = 0.024) and 1.34 (95% CI: 1.03-1.74, P = 0.030), respectively. The HR of moderate haematuria for mortality was 1.56 (95% CI: 1.11-2.20, P = 0.011). According to subgroup analysis, the HR of moderate haematuria for ESRD in patients with a UPCR of <500 mg/g was more prominent than that in patients with a UPCR of ≥500 mg/g. Microscopic haematuria in patients with stage 3-5 nondiabetic CKD is associated with increased risks of ESRD and mortality.