The purpose of this study was to evaluate the three-year clinical performance of a compomer and an amalgam in primary molars and to determine fluoride content in the enamel of these teeth after exfoliation. Twenty patients aged six to eight years randomly received one compomer and one amalgam restoration. Restorations were evaluated at baseline, 12, 24 and 36 months according to modified USPHS criteria. In six pairs of exfoliated teeth fluoride content at 1 and 5 mm distance from the restorations was determined. Replicas were made to determine marginal adaptation (MA) by scanning electron microscopy (SEM). At occlusal margins compomer restorations had better MA than amalgam restorations (p < 0.01). Compomer and amalgam restorations did not lead to different fluoride uptake in adjacent enamel and had an overall clinically satisfactory performance. The study confirmed that the assessed compomer is a suitable restorative material for class I and class II restorations in primary molar teeth.