Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was applied to the direct analysis of melamine cyanurate (MC). The three commonly used MALDI matrixes, namely, alpha-cyano-4-hydroxycinnamic acid (CHCA), sinapinic acid (SA), and 2,5-dihydroxybenzoic acid (DHB), were able to desorb/ionize melamine from MC upon N(2) laser irradiation, with CHCA showing the highest detection sensitivity in the positive mode. Only DHB and SA were able to desorb/ionize cyanuric acid from MC in the negative mode but with remarkably lower sensitivity. The method is able to detect melamine unambiguously from a small amount of MC (down to 12.5 microg) spiked into urine and was successfully applied for the rapid and sensitive detection of melamine in urine stones/residues of the samples collected from patients clinically confirmed of having kidney stones associated with the consumption of melamine-tainted food products. The urine matrix resulted in interfering ion peaks and suppressed the ion intensity of melamine, while a cleanup process consisting of simply washing with water eliminated such interference and enhanced the ion intensity. The merit of the method is simplicity in sample preparation. The analytical time of the method for high-throughput analysis from the time of sample treatment to analysis is less than 7 minutes per sample, with sensitive detection of the presence of melamine in the urine stones/residues of the patient samples.