Design Randomised controlled trial in a university setting.Intervention Children aged three to eight years, with at least one molar with an acute, deep carious lesion into the dentine were recruited. Treatment took place under rubber dam with decayed dentine being removed completely from the lateral walls of cavities in both groups using round burs operated at low speed. TCR or PCR was then performed in the pulpal wall of each tooth. After caries removal teeth were restored with calcium hydroxide cement and composite resin. Teeth with pulpal exposure were pulpotomised using ferric sulphate.Outcome measure The presence of a fistula, swelling, spontaneous pain and mobility not compatible with root resorption were considered to be clinical signs of failure. Radiolucency at the furcation or in the periapical region and internal or external pathological resorption were considered to be radiographic signs of failure.Results One hundred and twenty-four teeth in 51 patients were randomised. In the TCR group there were 57 teeth and 38 patients, with 41 patients and 67 teeth in the PCR group. Three patients (four teeth; one PCR and three TCR) dropped out leaving 120 teeth (PCR: n = 66; TCR: n = 54) for analysis. In the TCR group 27.5% (15) teeth in 13 children had pulp exposure compared with one tooth in one child in the PCR group (2%). The mean operative time was significantly higher for TCR (28.1 min; 95% CI: 23.6-32.6 min) than for PCR (17.9 min; 95% CI: 16.3-19.5 min). There was no statistical difference in success rates at 24 months between the groups. The success rate in the TCR group was 96%; (95% CI: 85-99%) compared with 92%; (95% CI: 81-96%) in the PCR group.Conclusions The clinical and radiographic success rates of PCR and TCR in primary teeth with deep carious lesions were high and did not differ significantly, indicating that PCR is a reliable minimally invasive approach in primary teeth and that the retention of carious dentine does not interfere with pulp vitality. Moreover, PCR provided other clinically relevant advantages over TCR, especially lower incidence of pulp exposure and lower operative time.