Mold surface temperature has a strong effect on the amount of molecular orientation and morphology developed in a non-isothermal flowing polymer melt. In this work, a well-characterized isotactic polypropylene was injected in a rectangular mold cavity asymmetrically conditioned by a thin electric heater specifically designed. The cavity surface was heated at temperatures ranging from 80 to 1608C for different times (0.5, 8, and 18 s) after the first contact with the polymer. Asymmetrical thermal conditions have a strong influence on the melt flow, by changing its distribution along the cavity thickness, and final part deformation. The morphology distribution of the molded samples was found strongly asymmetric with complex and peculiar features. Optical and Electron microscopy confirmed the complete reorganization of the crystalline structures along the sample thickness. X-rays analysis reveals that molecular orientation of the sample surface decreases with the mold temperature and the heating time.