The influence of annealing at temperatures where thermally activated crystallization rates become significant on the structural variations in the injection-molded polyethylene naphthalate (PEN) was investigated. In these studies, two distinct shear crystallized layers are observed. The shear crystallized layer near the skin forms during the filling stage, and the second shear crystallized layer forms during the packing stage but remains optically unobservable until the annealing takes place. Upon annealing, additional layers with larger crystallite sizes form around these preformed highly oriented layers. The alpha and beta phases were observed in both of the shear crystallized layers. The beta phase is generally grown either under high deformation fields or under quiescent conditions at high temperatures.