OBJECTIVE Aim of this randomised clinical trial was to compare the outcome of direct pulp capping (DPC) versus pulpotomy, both with MTA, for carious primary molars. METHODS Healthy, cooperative children aged 3-9 years with at least one deep carious primary molar requiring vital pulp therapy were included. Data on the primary outcome (all-cause failure) and secondary outcomes (clinical or radiographic failure) were collected blindly semi-annually for a minimum of 1 year up to 3 years and analysed with survival analysis and generalised linear regression at alpha = 5%. RESULTS A total of 74 children were randomly allocated on 1:1 basis to DPC (35 children; 40 teeth) or pulpotomy (39 children; 57 teeth). Survival from all-cause failure was 79.7% [95% confidence interval (CI) 69.3-86.9%] at 12 months and 66.0% (95% CI 53.4-76.0%) at 24 months which remained stable up to 36 months, with no differences between groups (P > 0.05). No significant difference was found in the survival rate of the two groups for all-cause [hazard ratio (HR) = 0.95; 95% CI 0.45-2.01; P = 0.88], clinical (HR = 0.74; 95% CI 0.0.19-2.92; P = 0.66), or radiographic failure (HR = 0.80; 95% CI 0.0.36-1.82; P = 0.60) throughout the 3-year follow-up. Regression analysis indicated that needing a second attempt for haemorrhage control was associated with higher clinical failure rate. All-case failure was significantly different for class II versus occlusal cavities and in the latter cavities pulpotomy performed better (P < 0.001). CONCLUSIONS The results of the current trial indicate that both DPC and pulpotomy can be reliable options for the treatment of deep carious primary molars in cooperative children, in carefully selected cases.