We set out to assess the effect of continuous ambulatory peritoneal dialysis (CAPD) and automated peritoneal dialysis (APD) on residual renal function (RRF) in children with end-stage renal disease (ESRD). In 101 children (age: 8.84 +/- 5.25 years; 44 on CAPD, 57 on APD) over 36 months, we evaluated RRF [as daily diuresis (DD) in mL/kg/24 h and mL/m2/24 h], glomerular filtration rate [GFR (in mL/min/1.73 m2)], ESRD cause, presence of arterial hypertension (HTN), biochemical parameters, peritoneal equilibration test (PET), adequacy [as total weekly Kt/V (twKt/V) and creatinine clearance (twCCr)], and infectious complications of PD. Initially, the CAPD and APD groups did not differ significantly in DD, but mean GFR was significantly higher in the APD group (p < 0.05). In the CAPD group, the volume of high osmolarity PD fluid was significantly lower (p < 0.05), and the rates of peritonitis and exit-site infection and of aminoglycoside use were higher (p < 0.001, p < 0.05, and p < 0.005 respectively). Over 36 months, the mean twKt/V and twCCr were within norms in both groups, but were higher in APD, significantly so (p < 0.05) for twKt/V at 24 and 36 months and for twCCr initially. In both groups, RRF decreased systematically, with a significantly lower (p < 0.05) rate of DD (mL/m2/24 h) and GFR decline in the first year in CAPD, but without a difference in the next 2 years. The longest RRF preservation was in children with tubulointerstitial nephropathies, particularly hypoplasia and dysplasia (p < 0.05). Children with hemolytic uremic syndrome (HUS) and hereditary nephropathy were at the highest anuria risk. Compared with the 22 children (7 CAPD, 15 APD) who became anuric, the 20 children (10 CAPD, 10 APD) with RRF preserved for 36 months had a higher DD and GFR before dialysis onset; higher hemoglobin and albumin; and lower HTN prevalence, cholesterol, triglycerides, and proteinuria (p < 0.05). Risk of anuria during 36 months did not differ significantly between the CAPD and APD groups. In children on CAPD or APD, risk factors for RRF loss include HUS, hereditary nephropathy, low diuresis and GFR before dialysis onset, HTN, anemia, hypoalbuminemia, hyperlipidemia, and proteinuria. Compared with children on APD, those on CAPD show better preservation of RRF during year 1, although the risk of anuria seems to be the same for both methods. In children with risk factors for rapid diuresis loss, CAPD might be considered the preferred initial dialysis method.