Cationic aliphatic ammonium polyionenes, specifically 12,12- and 6,12-ionenes, were synthesized using step-growth polymerization and aqueous-based size exclusion chromatography (SEC) coupled with multiangle laser light scattering (MALLS) revealed absolute molecular weight information. The chromatographic separation of cationic polyelectrolytes presents many additional challenges compared to SEC of nonassociating, neutral polymers. Therefore, an aqueous-based SEC-MALLS mobile phase composition was identified to separate these notoriously challenging polyelectrolytes in an effort to achieve absolute molecular weight analysis. Various solvent compositions were evaluated for their ability to solvate and reproducibly separate both 6,12- and 12,42-ionenes. Dynamic light scattering (DLS) verified the absence of aggregation of polyionenes in preferred mobile phase compositions. The optimum solvent composition comprised a tertiary mixture of 54/23/23 water/methanol/glacial acetic acid, 0.54 M NaOAc, at a pH of 4.0. Weight-average molecular weights for the synthesized ammonium 12,12-ionenes ranged from 11 000 to 40 000 g/mol, and ammonium 6,12-ionenes had weight-average molecular weights ranging from 19 000 to 49 900 g/mol. Mark-Houwink parameters were also determined for both the 12,12- and 6,12-ionenes in the optimum mobile phase using an online capillary viscometer.