A rapid screening simultaneously for alkaptonuria, ornithine carbamoyl transferase deficiency (OCTD) and neuroblastoma method was developed. Based on this method, the levels of individual markers for these diseases excreted in urine are measured. The chosen markers are homogentisic acid (HGA) for alkaptonuria; homovanillic acid (HVA) and vanillylmandelic acid (VMA) for neuroblastoma; orotic acid (OA) for Ornithine transcarbamylase deficiency (OTCD). Urine samples are diluted at 1/20 without any further sample preparation, then directly inject to a LC-MS system for quantitation. The linear dynamic range of quantitation for target components is made from 100 ng/ml to 250 ug/ml. The method was successfully used for screening patient urine in our hospital.