Objective To investigate the pathological features of yolk sac tumor(YST) in children, determine the immunohistochemical characteristics and their role in pathological diagnosis of YST, and discuss the differential diagnosis of YST. Methods The clinical data of 21 cases of YST were retrospectively summarized, among which 8 were concerned with gonad, and the other 13 nongonad. The characteristics of histology and immunohistochemical staining were observed. Results There were various pathological organizations for YST. There was micro capsule and reticular structure in 17 cases, embryo sinus structure in 16 cases, gland tube-gland bubble structure in 10 cases, papillary structure in 8 cases, giant cystic structure in 3 cases, intestinal type structure in 3 cases, polycystic bubble yolk sac sample structure in 2 cases and mucus tumor sample structure in 1 case. Immunohistochemical staining revealed that the positive expression rate of alphafetoprotein (AFP) was 95.24% (20/21), that of cytokeratin (CK) was 100% (21/21), and that of vimentin (Vim) was 76.19% (16/21). Conclusion Besides gonad (testis and ovary), YST in children can also involve non-gonad parts such as sacroiliac region, abdominopelvic cavity, cerebellum and soft tissues. The histological features of YST are diverse, which are characterized by the common structures such as micro capsule and reticular structure, inner embryo sinus structure, gland tube-gland bubble structure and papillary structure and rare structures such as giant cystic structure, intestinal type structure, mucus tumor sample structure and polycystic bubble yolk sac sample structure. Histomorphological characteristics and immunohistochemical findings may help to determine the pathological diagnosis and differential diagnosis of YST.