Polyacrylamide gel electrophoretic (PAGE) analysis ofFusarium infected cotton plants showed the disappearance of some erstwhile protein bands and the appearance of new bands to a greater degree in the compatible host-parasite combinations (Gossypium hirsutum/A1 strain;G. arboreum/I2 strain ofF. vasinfectum). Also, an increase in the number of antigenic proteins of the host following infection has been noticed only in the compatible host-parasite combinations as shown by agar double diffusion and immunoelectrophoretic studies. The newly formed antigens did not appear to originate either from the extracellular or intracellular protein pool of the pathogen; probably these are products of altered metabolism of the host species.