The structural characterization of a series of polyesters has been done by time-of-flight secondary ion mass spectrometry (TOF-SIMS) combined with transesterification. Polymer fragments and intact oligomers composed of large numbers of repeat units were observed. Transesterification of polyesters by trifluoroacetic acid (TFA) and chlorodifluoroacetic acid (CFA) was carried out to produce TOF-SIMS spectra. The shapes and intensities of clusters in transesterification spectra showed good agreement with theoretical isotope patterns. TOF-SIMS spectra were used to monitor the progress of the transesterification reaction. Transesterification products of branched poly(1,3-butylene adipate) were identified in the TOF-SIMS spectra, providing information about polymer branching.