We report matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and off-line coupling of size-exclusion chromatography with MALDI-TOFMS analysis (SEC/MALDI-TOFMS) methods for the detailed characterization of poly[(R,S)-3-hydroxybutyrate-co-L-lactic acid], P[(R,S)-3HB-co-LA], and poly[(R,S)-3-hydroxybutyrate-co-epsilon-caprolactone], P[(R,S)-3HB-co-CL], copolymer samples which are expected to be used in special medical application as scaffolds for cartilage and soft tissue engineering. The novel copolyesters contained randomly distributed (R,S)-3-hydroxybutyrate structural units, were synthesized by transesterification of the corresponding homopolymers, i.e. atactic poly[(R,S)-3-hydroxybutyrate], a-PHB, and poly(L-Lactide) (PLLA) or poly(epsilon-caprolactone) (PCL), respectively. The MS methods used for the characterization of the resulting polydisperse copolyester samples were supported by classical methods (NMR, SEC). The structures of individual copolyester macromolecules, including end-group chemical structures, were established using initially MALDI-TOFMS and then SEC/MALDI-TOFMS. The compositions of the copolyesters were determined by two methods, namely based on 1H NMR and MALDI-TOF spectra. The two sets of values showed good agreement. The sequence distribution was determined using the signal intensities of individual copolyester macromolecules, which appeared in MALDI-TOF mass spectra. Furthermore, sequence analysis gave information about the degree of transesterification. The copolyesters synthesized, with only one exception, were demonstrated to be almost random, which implies that the ester-ester exchange was close to completion.