In many organs, integrins and cadherins are partly regulated by Hox genes but their interactions in airway morphogenesis and congenital lung diseases are unknown. We previously showed that the Hox protein HoxB5 is abnormally increased in bronchopulmonary sequestration (BPS) and congenital cystic adenomatoid malformation (CCAM), congenital lung lesions with abnormal airway branching. We now report on alpha 2, alpha 3, and beta 1 integrin and E-Cadherin expression in normal human lung and in BPS and CCAM tissue previously shown to have abnormal HoxB5 expression and on the relationship of cell adhesion molecule expression to Hoxb5 regulation. Alpha 2, alpha 3, and beta 1 integrins, and E-Cadherin expression in normal human lung and BPS and CCAM were evaluated using Western blot and immunohistochemistry. Fetal mouse lung fibroblasts with Hoxb5-specific siRNA down regulation were evaluated for alpha 2 integrin protein levels by Western blot. Compared to normal human lung, a previously undetected alpha 2 integrin isoform potentially lacking essential cytoplasmic sequences was significantly increased in BPS and CCAM and alpha 2 integrin spatial and cellular expression was more intense. E-Cadherin protein levels were also significantly increased whereas alpha 3 increased in CCAM compared to canalicular but not to alveolar stage lung. Beta 1 integrin levels were unchanged. We conclude that in BPS and CCAM altered alpha 2 integrin cytoplasmic signaling contributes to abnormal cellular behavior in these lung lesions. Aberrant cell adhesion molecule and Hox protein regulation are likely part of the mechanism involved in the development of BPS and CCAM.