Objective To investigate the accuracy of anthropometric methods in assessing the body composition of children undergoing hematopoietic stem cell transplantation with direct segmental multi-frequency bioelectrical impedance analysis (DSM-BIA) as reference standard. Methods With prospective design, 65 children undergoing hematopoietic stem cell transplantation in Shanghai Children's Medical Center were enrolled. The body composition was measured by DSM-BIA, and the height, weight, mid upper arm circumference, triceps skinfold thickness and waist circumference were also recorded. Using DSM-BIA as reference standard, the accuracy of anthropometric measurements in assessing the body composition of children undergoing hematopoietic stem cell transplantation was tested. Results No matter in general or stratified by genders and mature status, triceps skinfold thickness had the highest correlation and minimal standard error with body fat percent measured by DSM-BIA (%BFDSM-BIA). Conclusion Triceps skinfold thickness is a favorable indicator in reflecting the body fat status of children undergoing hematopoietic stem cell transplantation.