The aim of this study was to estimate the structure of new polyurethanes with the potential to be used in medicine. Atactic poly[(R,S)‐3‐hydroxybutyrate], obtained via a ring‐opening polymerization, and polycaprolactonediol or polyoxytetramethylenediol were used to built the soft segments. 4,4′‐methylene dicyclohexyl diisocyanate and 1,4‐butanediol were the components to form hard segments. At FTIR spectra of obtained polyurethanes the bands attributed to NCO groups completely disappeared, similarly as these of OH groups and the new band characteristic for stretching vibrations of bonded urethane NH groups appeared. Polyurethanes with low‐molecular weight were obtained. The observation of FTIR and 1H‐NMR spectra had been suggested that NH groups form two types of hydrogen bonds: with CO urethane (possibly with ester group) and ether groups. An addition of poly[(R,S)‐3‐hydroxybutyrate] caused the slight increase in number of urethane–urethane hydrogen bonds. For some of polyurethanes (based on polyoxytetramethylenediol) the allophanate structures were obtained. © 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012