End-capped and intramolecular azofunctional oligocaprolactones were characterized at molecular level by liquid chromatography electrospray ionization mass spectrometry (ESI MS) and NMR spectroscopy. The Disperse Red 19 (DR19) azofunctional oligomers, DC, were synthesized by ring-opening oligomerization of e-caprolactone (e-CL) initiated by the hydroxyl groups of DR19 azo dye. The reaction products consist of a minor fraction of end-capped azo functional oligocaprolactone (a-DC), that is, a single CL arm oligomer, and a major fraction of intramolecular azo functional oligocaprolactone (b-DC), that is, a two CL arms oligomer. The chromatographic separation was used to discriminate between a-DC and b-DC, and the results were confirmed by MS/MS performed on an ESI ion trap instrument. The results supported by accurate mass data obtained for product ions using an ESI quadrupole time of flight instrument demonstrate the qualitative discrimination at the molecular level between intramolecular and end-capped azofunctional oligoesters isomers through a relatively simple multistage mass spectrometry experiment.