Perfluorinated sulfonic acid polyelectrolyte aqueous dispersions originating from similar polymer feed stocks and having similar compositions can have order-of-magnitude viscosity differences that are dependent on the manufacturing process. To better understand this phenomenon at the molecular level, a size exclusion chromatography method incorporating static light scattering detection was developed. The initial apparent mass distributions were broad and bimodal for all dispersions. A high-molar-mass shoulder was consistent with a previously postulated aggregate structure, and the evidence suggested that molecular aggregation accounted for viscosity variability. The apparent weight-average molar masses ranged from 1.3 x 10(6) to 3.9 x 10(6) g mol(-1). Upon the heating of the dispersions at or above 230 degreesC, the aggregate structure was broken down, and this resulted in similar low-viscosity dispersions that had monomodal mass distributions. The weight-average molar masses were reduced to approximately 2.5 x 10(5) g mol(-1), and the polydispersities were approximately 1.7-1.8. Shear thinning with higher viscosities and apparent molar masses was rationalized with intrinsic viscosity and other measurements, which supported an anisotropic aggregate structure, with particles that could be significantly overlapped at nominal 11% concentrations. (C) 2005 Wiley Periodicals, Inc.