Using PCR, six genes of the HOM/HOX class have been identified in hydra. One of them, Cnox-2, has been sequenced and resembles the Deformed gene of Drosophila. As shown previously, the expression pattern of Cnox-2 suggested that it may be involved in axial patterning as it was strongly expressed in the epithelial cells of the body column and foot, but only weakly expressed in the head. In addition, expression of Cnox-2 decreased sharply in body column tissue as it was converted into head tissue, thereby providing further support for a role in hydra pattern formation. To examine this possibility further, additional manipulations were carried out which convert body column tissue into either head or foot tissue. When body column tissue was converted into head tissue by regeneration, transplantation, or during budding, Cnox-2 expression was sharply reduced, indicating that expression of this gene is suppressed during head formation. When body column tissue was converted into foot tissue by regeneration or Li+ treatment, the changes in Cnox-2 expression patterns indicated that Cnox-2 had no direct role in foot formation. Surprisingly, however, the observed changes in Cnox-2 expression patterns indicate that following bisection, both head and foot regeneration processes are initiated at the injured edge of the bisected animal.