In this work, an attempt is made to simulate the skin temperature profile of breasts in the presence of Cysts. For the first time a study comparing the temperature profiles of normal breasts with Breast Cysts is undertaken. Heat transfer mechanism is modelled as the Penne's Bio-heat equation on 2D breast sections. The equation is solved using the Finite Element Method. The Cysts are simulated for typical depths and sizes. It is observed that for Cysts at depths greater than 5 cm and of sizes less than 0.5 cm the effect on the surface temperature is negligible. It is also found that in all configurations surface temperature drops. Cyst of maximum radius when placed closest to the skin surface, the temperature declines the most. Therefore this study seems to help in reducing the false positive rate during screening and in the early diagnosis of breast cancer using infrared imaging. © 2014 IEEE.