Differentiation of embryonic stem cells is of great interest to developmental biology and regenerative medicine. This study investigated the effects of cytochalasin D (CD) on the distribution of actin filaments in mouse embryoid body (EB)-derived cells. Furthermore, CD was applied to chondrogenic medium to examine its chondrogenic effect. CD at a concentration of 1 microg/ml disrupted stress fibers in EB-derived cells. Actin filaments in treated cells reorganized into a peripheral pattern, and type II collagen was detected by immunocytochemistry. The expression of type II collagen, Sox9, and at a later time point, aggrecan was up-regulated after CD treatment. In the CD-treated cells, Oct4 and Sox2, representing undifferentiation, were down-regulated as well as Sox1, AFP, and CTN-1, representing ectoderm, endoderm, and cardiogenesis, respectively. In conclusion, CD treatment enhances chondrogenesis of EB-derived cells. Moreover, it promotes a more complete stem cell differentiation toward chondrogenesis, when cultured in chondrogenic medium.