Heterocyclic amines (HAs), generated when proteinaceous food is cooked, are of special interest since they can be carcinogenic for humans. In this paper, the optimization of a clean-up procedure for the isolation and preconcentration of 15 heterocyclic amines in urine samples is described. The method proposed combines liquid extraction on a solid support of diatomaceous earth with solid-phase extraction in cartridges. Tests were performed on several cartridges containing graphitic carbon or mixed phases, i.e., combining reversed-phase and cation-exchange mechanism, and the best results were obtained with Oasis MCX. The optimized purification method was applied to the quantification of heterocyclic amines in hydrolyzed spiked human urine. The method was carried out by capillary electrophoresis (CE) coupled to mass spectrometry (MS) and applying field-amplified sample injection (FASI) as in-line preconcentration procedure. We obtained detection limits down to 0.3 ng/ml of urine and errors lower than 17%.