The predominant isoform of glial fibrillary acidic protein (GFAP), GFAPalpha, is the characteristic building block of the cytoskeletal intermediate filaments in astrocytes. Isoform GFAPepsilon, produced by alternative splicing of the GFAP gene, includes a new tail domain that confers a presenilin binding capacity. We here show that the GFAPepsilon tail prevents GFAPepsilon homodimerization and homomeric filament formation, whereas the ability to form heterodimers and filaments with GFAPalpha is retained. Furthermore, GFAPepsilon shows decreased affinity for several GFAPalpha-interacting proteins. A GFAPepsilon tail mutation that results in gain of GFAPepsilon dimerization and filament formation abolishes presenilin binding. This mutation also abolishes interaction between the tail and the coiled-coil domain of GFAPepsilon. Together, this indicates that direct interaction between the coiled-coil and tail domains may serve as an inhibitory mechanism for homomeric dimerization and filament formation. We propose that the GFAPepsilon isoform represents a new functionally distinct component of GFAP intermediate filaments.