Substrate material used in microstrip antenna structures fully impact the performance of antenna and applications of it. In this work, simulations are carried out for microstrip antenna structure used in biomedical applications. Heart vessel structure used for determining heart diseases is modelled in Ansoft HFSS program. Simulations are implemented with and without occlusion in heart vein. Antenna structure is simulated with different substrate materials and different thicknesses of them. After simulations, various electromagnetic field data are obtained and evaluated for dissimilar substrate materials and thickness of them.