Thermal and rheological properties of various blends of gelatinized starch and biodegradable polyester polycaprolactone (PCL) or poly(butylene succinate adipate) (PBSA), were studied by DSC, TGA and rheometry. Methylenediphenyl diisocyanate (MDI) was used as a compatibilizer and was distributed indifferent phases through controlled processing. The addition of MDI showed a stronger effect on thermal and rheological properties when it was mainly distributed in the polyester phase prior to blending. Starch was shown to increase the shear viscosity of both types of polyesters. The two blends, starch/PCL and starch/PBSA, showed a similar pattern of a power law dependence of viscosity on shear rate. MDI was shown to enhance the effect of starch on the melting and decomposition temperatures, especially when distributed in the polyester phase.