The degradation induced by MeV He+ ions onto polyethylene terephthalate (PET) is investigated as a function of fluence and electronic stopping power (dE/dx)e. Stack samples of four 3.6μm PET films are irradiated by 3.5MeV He+ under vacuum and room temperature at fluence ranging from 1013 to 1.5×1015He+cm−2. The entrance energies range from 3.5MeV for the front film to 0.573MeV for the rear one at the beginning of the irradiation and the corresponding mean (dE/dx)e lie for pristine PET between 158 and 264keV/μm. A Fourier transform infrared spectroscopy (FTIR) analysis is undertaken. The different stack films present similar damages with magnitude increase as the fluence goes up. Moreover, higher is the electronic stopping power (dE/dx)e more important is the damage. The evolution of the normalized integrated absorbance A(ϕ)/A0 of the internal reference 1410cm−1 band as a function of the fluence ϕ presents a complex behavior characterized by a two-exponential decay associated to low and high fluence range. The analysis reveals clearly that the A(ϕ)/A0 of the characteristic benzene ring 1577cm−1 band remains steady till fluence around 3×1014He+cm−2 and then decreases smoothly as fluence increases. The band appearing at 1610cm−1, assigned to mono substituted benzene, presents an integrated absorbance A(ϕ) which rises progressively and levels off beyond a critical fluence around 4×1014He+cm–2. The cross section of the creation of the monosubstituted benzene lies between 3×10−15 and 6×10−15cm2 for (dE/dx)e=158 and 264keV/μm, respectively.Drastic loss of crystallinity is induced by the MeV He+ ion irradiation in the polymer. The amorphization is monitored by the evolution of the specific bands of the trans and gauche ethylene glycol residue conformations. A sudden drop in the integrated absorbance of the 1340cm−1 band which characterizes the trans conformation is observed at fluence around 2×1014He+cm−2. On the other hand, a drastic increase is present in the integrated absorbance of the gauche conformation 1370cm−1 band that pairs up with 1340cm−1 band. This observation is a clear indication of the conversion of the trans ethylene glycol residue to gauche one under irradiation.