Niemann-Pick disease type C (NPC) is a neurodegenerative autosomal recessive disorder accompanying with accumulation of cholesterol. The diagnostic of NPC is difficult due to the diversity of the phenotype and the age of onset, and the current definitive diagnostic methods have some problems. Therefore, a simple and rapid diagnostic method for NPC is required. We have previously developed an LC/ESI-MS/MS method for three NPC characteristic urinary metabolites, 3β-sulfooxy-7β-N-acetylglucosaminyl-5-cholenoic acid and its glycine- and taurine-amides (SNAG-Δ5-CA, SNAG-Δ5-CG and SNAG-Δ5-CT). In this study, we evaluated the diagnostic performance of the method for NPC. SNAG-Δ5-CA and SNAG-Δ5-CG in urine from NPC patients were significant higher than the healthy controls. In ROC analysis, they all showed the good performance. In addition, we analyzed urine samples to find other diagnostic marker candidates by a focused metabolomic method for conjugated cholesterol metabolites.