In this work, isothermal crystallization kinetics of polyoxymethylene copolymer (POM) in POM/hydroxyapatite (HAp) nanocomposites has been investigated. Melting behavior and crystalline structure formation were studied using TOPEM DSC, positron lifetime spectroscopy (PALS), atomic force microscopy (AFM) and 13C and 31P solid‐state NMR. The highest degree of crystallinity was found for POM/0.5% HAp nanocomposite and the lowest for POM/2.5% HAp. Isothermal crystallization analysis showed that an introduction of HAp nanoparticles led to effective heterogeneous nucleation and formation of crystals with higher Avrami exponent. Besides, changes in overall crystallization rate were observed – the highest overall crystallization rate was found for POM/0.5% HAp sample, while the lowest for POM/2.5% HAp was observed. Generally, for POM in POM/HAp nanocomposites, a significant decrease in nucleation activation energy (Kg), and the fold surface free energy (σe) was found. For nanocomposite containing 2.5% HAp, heterogeneous nucleation takes place as well, but too high concentration of nanoparticles hinders POM crystallization and enhances formation of more defected crystals as confirmed by AFM data. The presence of HAp nanoparticles in the POM matrix was confirmed by 31P MAS‐NMR, but their influence on the crystallization process was not observed in the 13C CP‐MAS‐NMR spectra. Copyright © 2012 John Wiley & Sons, Ltd.