The properties of blends, cast from hexafluoro-2-propanol; of nylon 6 and of nylon 12 with polyaniline doped with various functionalized organic acids were investigated using differential scanning, calorimetry and microscopy. The glass transition temperature of the as-cast and dried blends;ls of polyaniline with either nylon displayed a composition-independent relationship indicative of a phase-separated morphology irrespective of the functionalization of the sulfonic acid dopant. Although electron microscopy data also showed phase-separated morphologies, the PANI domain size within the nylon matrix was found to be dependent upon the functionalized acid dopant. A decrease in the melting transition temperatures of nylon 6 and associated enthalpies with blend composition is attributed to the effects of dissociation and degradation processes occurring during thermal analysis. We suggest that the effusion of the resulting thermally induced species from within the polyamide domain disrupts the crystalline structure, leading to depression in the melting point and heat of fusion. Changes in other thermal transitions, such as melt and cold crystallizations and their enthalpies, were attributed similarly to products of PANI dissociation and degradation formed during thermal analysis.