In this work, the effect of processing and subsequent thermal treatment on the rheological behavior and microstructure aggregation of two different types of thermoplastic polyurethanes (TPUs) are investigated. Elastomeric TPUs, which are segmented block copolymers composed of alternating soft and hard segments, and amorphous glassy TPU, predominantly composed of hard segments, were subjected to heating/cooling cycles after extrusion. All materials show rheological hystereses after the first thermal cycle; in amorphous glassy TPUs, there is an increase in dynamic moduli but the loss tangent remains unchanged, whereas in the elastomeric TPUs, there are both decreases in dynamic moduli and hystereses in the loss tangent. The changes in molecular weight during the thermal cycle were tracked by gel permeation chromatography and shown not to be responsible for the rheological hystereses. For both elastomeric and amorphous glassy TPUs, fourier transform infrared spectroscopy results indicate that an increase in dynamic moduli, especially G′, is associated with a higher degree of hydrogen bonding. These results combined with X‐ray data indicate that upon extrusion the elastomeric TPUs form a network in which hydrogen bonding plays an important role. This structure can be disrupted upon subsequent heating and cooling. POLYM. ENG. SCI., 54:1383–1393, 2014. © 2013 Society of Plastics Engineers