The global protein patterns in normal and aborted embryo of litchi at 40 days after flowering (DAA) were compared by using two-dimensional polyacrylamide gel electrophoresis (2-DE) and computer image analysis. The results showed that the quantities of 100 protein spots in normal embryo were significantly different from aborted embryo. There were 15 and 50 spots appeared on the gel of normal embryo and aborted embryo, respectively. Then they were selected for MALDI-TOF-MASS analysis. Nine proteins related with embryo development were identified, which maight involve in regulating and controlling the embryo abortion.