We report on the isolation of two bovine cardiac troponin isoforms which differ in sequence near the amino terminus of troponin T (Risnik, V. V., Verin, A. D., and Gusev, N. B. (1985) Biochem. J. 225, 549-552). The isoforms were isolated by direct separation on DEAE-cellulose and were also obtained by reconstitution of urea-dissociated subunits. The two isoforms were compared for their effects on processes involving interactions of troponin with tropomyosin and actin. The two isoforms had similar abilities to promote tropomyosin polymerization. They allowed equal potentiation, by high concentration of myosin subfragment 1, of the thin filament-activated MgATPase rate. In the presence of lower concentrations of myosin subfragment 1, the MgATPase rate was 96% sensitive to Ca2+, regardless of which troponin isoform was present. The Ca2+ concentration required to activate the MgATPase rate was similar but not identical for thin filaments containing one isoform or the other. In the presence of the smaller isoform, the Ca2+-activation curve is shifted 0.1 to 0.15 pCa units to the left. At 10(-6) M Ca2+ the MgATPase rate is 50% greater when the smaller troponin T isoform is present than when the larger is present. These results indicate that the variable region of troponin T influences the overall response of the thin filament to Ca2+, and raises the possibility that regulation of this region by mRNA splicing may modulate muscle function.