In the axonemes of Tetrahymena cilia, beta-tubulin was digested more rapidly by chymotrypsin than alpha-tubulin. On the other hand, in the solubilized state, both tubulins were digested by the protease at almost the same rate. Among alpha-tubulin isotypes within the axonemes, alpha 5-tubulin was more rapidly digested by chymotrypsin than other alpha-tubulin isotypes. The addition of ATP and vanadate (Vi) to the axonemes significantly protected the alpha 5-isotype from chymotryptic proteolysis. These tendencies could not be observed in tubulins solubilized from axonemes. Based on the case of the alpha 5-tubulin isotype, it is possible to negate the idea that all tubulin isotypes are distributed homogeneously and play similar functional roles within the axonemes.