The overall goal of the present study was to identify the high molecular weight species formed during the synthesis and processing of polymeric methylene diphenyl diisocyanate (PMDI) and determine the root cause of the viscosity buildup in these materials. Initial studies focused on the use of MALDI-TOF mass spectrometry to examine the PMDI mixture and MALDI-TOF/TOF CID fragmentation for elucidating the degradation mechanisms of the identified compounds. The low molecular mass portion of the MALDI spectrum was observed to contain the expected PMDI and small quantities of carbodiimides (CDIs). The high molecular mass portion of the spectrum primarily contained 1,3-diazetidine branched carbodiimide dimers, uretonimine branched CDIs, and imino-s-triazine along with low levels of guanidine branched CDIs. The results of this study indicate that the root cause of the observed CDI defects was extensive branch formation through unexpected side reactions catalyzed by iron(III). These reactions lead to a buildup of viscosity which poses a significant challenge during the processing of these materials.