The mechanisms controlling the elution of carboxylated polyurethanes (CPUs) and polyurethane ionomers (PUIs) during the size exclusion chromatography (SEC) separation process in tetrahydrofuran (THF) were investigated. In order to elucidate the elution process, their dilute solution viscosity behaviour was studied as well. Sample molar mass averages were determined by SEC using polystyrene calibration (SEC-PS) and in the case of CPUs also by SEC coupled with a multi-angle light scattering detector (SEC-MALS). The molar mass averages and intrinsic viscosities of CPUs decrease with increasing degree of carboxylation as a consequence of side-reactions. The large difference in reduced viscosity between non-carboxylated PU and CPUs can be attributed to different macromolecular conformations in THF solution. The molar mass averages of PUIs determined by SEC-PS were much lower than those of the parent CPU and showed a slight dependence on the type of counterion used. In the selected series, the molar mass averages and intrinsic viscosities increased in the order Ca2+ < Li+ < Na+ < K+. The addition of CF3COONa had no influence on the solution viscosity of CPUs, while it prevented the association of PUIs.