Abstract The double endothermic behaviour of poly(aryl ether ether ketone) (PEEK) has been the subject of considerable debate during the last few years. In this paper, the various explanations for the double endothermic behaviour of PEEK are examined using a combination of real time small angle X-ray scattering (SAXS) and differential scanning calorimetry (d.s.c.) techniques. The correlation function approach was used to analyse SAXS data. The correlation functions were interpreted in terms of a two-phase model to obtain average lamellar and amorphous, layer thicknesses. The average lamellar and amorphous layer thicknesses are observed to be about 125Å and 50Å respectively. From the SAXS data, it is observed that the average amorphous layer thickness (1) does not decrease during the development of the low endotherm, and (2) decreases during melting at temperatures corresponding to the low endotherm. From the d.s.c. studies, it is observed that the high endotherm develops before the low endotherm. Based on these and other observations, the melting recrystallization model and the lamellar insertion model are ruled out as possible explanations for the origin of the low endotherm in PEEK. We suggest that the origin of the low and high endotherms lies in melting of secondary and primary lamellar stacks respectively. The secondary lamellar stacks consist of thinner lamellae and thicker amorphous layers as compared to the primary lamellae which results in the high endotherm.