The aim of this work is to determine the relaxation times of the cooperative conformational rearrangements of the amorphous phase in semi-crystalline poly(ethylene terephthalate) (PET) and compare them with those calculated in amorphous PET. Samples of nearly amorphous polymer were prepared by quenching and samples with different crystallinity fractions were prepared from the amorphous one using cold crystallisation to different temperatures. The differential scanning calorimetry (DSC) thermograms measured on samples rapidly cooled from temperatures immediately above the glass transition show a single glass transition which is much broader in the case of high-crystallinity samples than in the amorphous or low-crystallinity PET. To clarify this behaviour, the samples were subjected to annealing at different temperatures and for different periods prior to the DSC measuring heating scan. The thermograms measured in samples with low crystallinity clearly show the existence of two amorphous phases with different conformational mobility, these are called Phases I and II. Phase I contains polymer chains with a mobility similar to that in the purely amorphous polymer, while Phase II shows a much more restricted mobility, probably corresponding to conformational changes within the intraspherulitic regions. The model simulation allows to determine the temperature dependence of Phase II relaxation times, which are independent from the crystallinity fraction in the sample and around two decades longer than those of the amorphous polymer at the same temperature.