The microstructures of amorphous and crystalline poly(ethylene terephthalate) (PET) homopolymers have been determined in terms of their trans and gauche conformational isomer contents by using a combination of infrared and density characterization techniques. The effects of isothermal crystallization (from the glassy state between 105-150 degrees C), as well as the effects of different monomer units in the polymerization process, have been investigated. Results indicate that samples, polymerized from different monomer and catalyst systems, show different microstructures in terms of trans and gauche isomers. These variations result in significant differences in PET optical properties. Further investigations find that these dissimilar behaviors accompany conformational isomer variations in the amorphous phase, suggesting different transformation mechanisms of trans and gauche isomers at early stages of crystallization. These unlike microstructural transformation processes give rise to further changes, which are evidentin terms of the intensity of Vv light scattering, haze values, thermal properties, and FTIR spectral results.