Neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) is a novel inborn error of metabolism due to dysfunction of citrin protein, and much more information about this new disease is still needed for its clinical management. To investigate in detail the clinical and laboratory features of NICCD. 13 NICCD subjects in mainland of China diagnosed in our department since 2006. The anthropometric parameters of the patients at birth were compared with controls, representative biochemical changes and metabolome findings were investigated cross-sectionally, and mutations in the causative gene SLC25A13 were analyzed by protocols established previously. The patients showed reduced birth weight, length and ponderal index. Main clinical manifestations consisted of jaundice, hepato/hepatosplenomegaly and steatohepatosis on ultrasonography. Biochemical analysis revealed intrahepatic cholestasis, delayed switch of AFP to albumin, and elevated triglyceride, total cholesterol and LDL-cholesterol together with reduced HDL-cholesterol. Metabolome findings included co-existence of markers for galactosemia and tyrosinemia in urine, and elevated Cit, Met, Thr, Tyr, Lys, Arg and Orn in blood. Mutations of 851-854del, IVS6+5G>A, 1638-1660dup, A541D, IVS16ins3kb, R319X and G333D were detected in the gene SLC25A13. The diagnosis of NICCD cannot be established based just on the numerous but non-specific clinical manifestations and biochemical changes. The relatively specific metabolome features provide valuable tools for its screening and diagnosis, while SLC25A13 mutation analysis should be taken as one of the reliable tools for the definitive diagnosis. The body proportionality at birth, steatohepatosis on ultrasonography, delayed switch of AFP to albumin, dyslipidemia pattern, urinary metabolome features and the novel mutation G333D expanded the clinical spectrum of NICCD.