Nutritional status of 380 hospitalised children aged from 1 month to 5 years with liver disease was evaluated in a single paediatric centre. The total prevalence of stunting (height-for-age Z (HAZ) < −2), underweight (weight-for-age Z (WAZ) < −2) and wasting (weight-for-height Z < −2) was 9·8, 9·0 and 7·9 %, respectively. The overall nutritional risk (−2 ≤ Z < −1) of stunting, underweight and wasting was 11·8, 12·9 and 12·6 %. The prevalence of undernutrition was significantly higher in children with cholestasis than children without cholestasis (stunting, 17·5 %/4·4 %, P < 0·001, and underweight, 14·9 %/4·9 %, P < 0·001). HAZ and WAZ scores were significantly higher in children without cholestasis than children with cholestasis (0·58 (sd 1·59)/−0·68 (sd 1·99), P < 0·001, and 0·37 (sd 1·35)/−0·47 (sd 1·75), P < 0·001). Further multivariate logistic regression analysis strengthened the evidence that cholestasis was significantly associated with undernutrition of stunting (OR = 4·18, P = 0·002) and underweight (OR = 3·26, P = 0·008), and suggested that the prevalence of stunting caused by infection was lower than other aetiologies in hospitalised children with liver disease (OR = 0·10, P = 0·002). We concluded that a high prevalence of malnutrition and risk of undernutrition presents in hospitalised young children with liver disease, especially in children with cholestasis. Nutrition assessment is recommended for hospitalised children with liver disease.