High-temperature atomic force microscopy (AFM) was used for in-situ monitoring of melt-crystallization of poly(ethylene terephthalate) (PET) at 233 degreesC. The observed evolution of the lamellar structure allowed identification of the stack thickening process at the secondary crystallization stage. This finding explains the puzzling decrease of the small-angle X-ray scattering (SAXS) long period observed during isothermal annealing of PET. The quantitative analysis of high-temperature AFM images provides statistically meaningful parameters for the semicrystalline structure and an accurate choice of a structural model for the interpretation of SAXS data.