Improvements in the antithrombogenicity activity of biomaterials for cardiovascular applications are necessary to meet the demand for vascular grafts in the world. Zwitterionic compounds tend to be used due to their anti-fouling properties, which reduce platelet adhesions and protein absorptions. Therefore, in this research, potato starch (AL-N) and zwitterionic starch (AL-Z) (obtained by Williamson etherification) were included as fillers in polyurethane (PU) matrices from polycaprolactone diol (PCL), polyethylene glycol (PEG), pentaerythritol (PE) and isophorone diisocyanate (IPDI) in order to study their effect in terms of their physicochemical, mechanical and thermal properties. We conducted our evaluation using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), contact angle analysis, swelling behavior, thermogravimetric analysis (TGA), tensile/strain analysis, scanning electron microscopy equipped with energy dispersive X-ray spectroscopy (SEM-EDS), dynamic mechanic analysis (DMA), differential scanning calorimetry (DSC), and X-ray diffraction (XRD). The results showed that AL-N and AL-Z modified these properties, where AL-N improved tensile strength, and AL-Z increased the hydrophilicity of polyurethanes matrices; additionally, AL-N had interactions with the soft segments, and AL-Z had interactions with the hard segments. Finally, both fillers reduced the degree of crystallinity and did not affect the thermal stability of polyurethanes.