Mycobacterium avium is capable of invading the intestinal epithelial cells, which requires cytoskeleton rearrangement and protein phosphorylation in the host cell. However, little is known about the mechanism. A transposon bank was screened for invasion-impaired mutants. Among the genes identified, inactivation of the fadD2 gene resulted in approximately 50% reduction in invasion in vitro and 100-fold reduction in invasion in vivo, compared with the wild-type (wt) strain. Invasion by wt M. avium led to the recruitment of neuronal Wiskott-Aldrich syndrome protein (N-WASp), which was not observed with mutant lacking a functional fadD2 gene. M. avium entry resulted in the phosphorylation of N-WASp and activation of the Arp2/3 complex. Supernatant obtained from wt M. avium incubated with HEp2 epithelial cells rescued the mutant 1B2 ability to enter the cells, which suggests that activation of Cdc42 probably follows the secretion of M. avium proteins. fadD2 is a regulator of M. avium invasion, and its effect is through Cdc42.