This study was aimed to establish the protein expression profile of tel/aml-1+ childhood acute lymphoblastic leukemia (ALL) with different prognoses by two-dimensional polyacrylamide gel electrophoresis and explore the nosogenesis of tel/aml-1+ ALL childhood. On the basis of leukocyte count at new diagnosis, early reaction to therapy and clinical prognosis, the patients with tel/aml-1+ ALL were divided into 3 groups: early relapse group, high leukocyte count group and standard risk group. The bone marrow was taken from newly diagnosed patients for isolating protein, then the protein in leukemia cells was isolated by two-dimensional polyacrylamide gel electrophoresis, the image analysis of differential protein among 3 groups was carried out by using the PDQuest 7.3.0 image analysis software. The results showed that there were significant difference of protein expression profile among 3 groups. As compared with high leukocyte count and standard risk groups, 71 protein spots disappeared, 93 new protein spots appeared, the expression of 37 protein spots was up-regulated and the expression of 23 protein spots was down-regulated in early relapse group. As compared with high leukocyte count group, 6 protein spots disappeared, 56 new protein spots appeared, the expression of 7 protein spots was up-regulated, and expression of 19 protein spots was down-regulated in standard risk group. It is concluded that the protein expression profile in early relapse group is significantly different from other groups. Some proteins may play an important role in pathogenesis of childhood tel/aml-1+ ALL, and probably become new molecular indicators and targets for individualized treatment.