Objective To better understand Rotor syndrome(RS)in children,the clinical features and SLCO1B1 and SLC01B3 gene mutations were analyzed. Methods The clinical data of the 3 pediatric cases diagnosed in Guangzhou Women and Children's Medical Center between 2018 and 2019 was collected. Genomic DNA was extracted from the children and their family members, and subjected for second-generation sequencing to screen the known genes for liver genetic metabolic diseases. Then the detected mutations were confirmed by Sanger sequencing analysis. Results The main clinical manifestations were recurrent or persistent mild yellowish sclera and/or skin. Laboratory examinations showed hyperbilirubinemia with direct bilirubin elevating. Second generation sequencing showed that all 3 children were c.1738c＞Thomozygous mutations of SLCO1B1 gene and homozygous mutations of large fragment insertion in SLCO1B3 gene intron 5. Two homozygous mutations in SLCO1B1 gene and SLCO1B3 gene were verified in families.SLCO1B1 gene c.1738C＞T mutation,a nonsense mutation reported in references,could lead to protein function loss.A large insertion mutation of SLCO1B3 gene could cause frame-shift mutation which might lead to protein function loss even though it was neither reported in the references nor recorded in SNP database. Conclusion Due to the progress in the clinical application of gene detection technology, RS has been recognized gradually by pediatricians. Homozygous mutations or compound heterozygous mutations simultaneously occurred in SLCO1B1 and SLCO1B3 gene were the molecular genetics base in these cases of RS.