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An attempt was made to explore the effects of the interchange reactions on the viscoelastic behavior of binary blends based on poly(ethylene terephthalate) (PET)/poly(ethylene naphthalate) (PEN) and their nanocomposites. It was seen that with an increase in the number of extrusion runs and mixing temperature, the extent of reaction (X) and degree of randomness (RD) both increased, whereas the average sequence block lengths values were decreased. On the contrary, the blend composition did not play a significant role on X and RD values. Addition of nanoclay inhibited the transreactions in PET/PEN blends. The absence of crystallization peaks implied that the crystalline structure was destroyed as a result of blending and an amorphous system was created possibly due to the transreactions simultaneously with the formation of random copolymers inhibiting the crystallization process. The rheological investigations showed that the addition of PEN into the PEN/PET blends enhanced the storage modulus, loss modulus, and complex viscosity. The viscosity upswing observed at low-frequency region in the case of nanocomposite systems evidently confirmed the occurrence of transreactions. Nonetheless, a significant increment in the viscoelastic properties was perceived in the presence of nanoclay corroborating the proper nanoclay distribution throughout the PET/PEN blend system. POLYM. ENG. SCI., 53:2556–2567, 2013. © 2013 Society of Plastics Engineers