Atraumatic Restorative Treatment, ART, is a method of minimal caries intervention that uses only hand instruments. The aim of the present study was to explore a possible difference between the extent of discomfort experienced during dental treatment according to the ART approach and a method using rotary instruments. The study was performed in Indonesia. A total of 403 children were randomly divided in two groups. In each child, one class II restoration in a deciduous molar was made. One group received treatment using rotary instruments (750 r.p.m.). The other group was treated according to the ART approach. Glass ionomer cement was used for restoration in both groups. Discomfort scores were determined using both physiological measurements (heart rate) and behavioral observations (Venham) on specific moments during the treatment. Venham scores showed a marked difference between the two groups at most time points. Heart rate measurements were different at deep excavation. Also, a clear relation between Venham scores and heart rate measurements could be found at all time points. Confounding could be shown for operating dentist, gender of the patient and initial anxiety, not for age. No effect modification could be shown. It can be concluded that children treated according to the ART approach using hand instruments alone experience less discomfort than those treated using rotary instruments.