Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used in combination with size exclusion chromatography (SEC) to characterize a series of copolyesters with butylene adipate (BA), butylene succinate (BSu), and butylene sebacate (BSe) units. These copolyesters, synthesized by condensation polymerization from 1,4-butanediol and dimethyl esters, have flexible chains, are random, and do possess a homogeneous composition. The SEC fractionation of these polymers allowed to collect numerous fractions that were then analyzed by MALDI-TOF. The mass spectra of these nearly monodisperse fractions allowed the computation of the corresponding molar masses (MM). The calibrated SEC traces could then be used to compute average MM and molar mass distribution of the unfractionated samples. Furthermore, the SEC/MALDI data allowed an estimate of the effect of the hydrodynamic interactions of comonomers A and B along the copolymer chain and a comparison with the theoretical predictions. Sensible deviations from the simple additivity have been found for the four copolymers studied.