Abstract Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to deduce the three-dimensional structure of a complex silsesquioxane polymer. Four distinct levels of structure were observed in the mass spectrum. The overall shape of the peak distribution was typical of polymers formed by condensation reactions. The mass separation between major clusters of peaks, each major cluster corresponding to an oligomer with a unique number of repeat units, confirmed that the synthesis proceeded as expected with no side reactions. The mass separation between peaks within a major cluster showed that intramolecular reactions during synthesis resulted in the elimination of water. The loss of water was ascribed to the formation of closed loops in the polymer structure. A simple arithmetic algorithm is presented for identifying these peaks. Autocorrelation techniques were used to determine the number and distribution of intramolecular closed loops per oligomer. This knowledge was used to deduce whether a particular oligomer is branched-linear, ladder, polyhedral, or some combination of these. The single-oligomer isotopic distribution was used to determine that cationization was present from both sodium and potassium ions.