Aggregation of the amyloid-beta protein (A beta) contributes to the neurodegeneration characteristic of Alzheimer's disease. Of particular importance are the early stages of aggregation, which involve the formation of soluble oligomers and protofibrils. In these studies, we demonstrate the potential for CE with UV detection using a polyethylene oxide separation matrix to identify the evolution of various oligomeric species of A beta(1-40). To demonstrate the efficacy of this technique, UV-CE was utilized to compare two methods commonly used to prepare A beta for aggregation experiments and their effect on the formation of early aggregates. SEC-purified A beta(1-40) initially contained more small species, including monomer, than did freshly dissolved A beta(1-40) pretreated with hexafluoroisopropanol. Strikingly, the lag time to oligomer formation for SEC-isolated A beta(1-40) samples was similar to 23 h shorter compared to freshly dissolved A beta(1-40) samples. Furthermore, oligomers formed from the aggregation of SEC-purified A beta(1-40) persisted within solution for a longer period of time. These results indicate that the initial sample preparation has a drastic influence on the early stages of A beta(1-40) aggregation. This is the first report of the use of UV-CE with a separation matrix to study the effect of sample preparation on early aggregation of A beta(1-40). UV-CE was also used in parallel with dot blot analysis and inhibitory compounds to discern structural characteristics of individual oligomer peaks, demonstrating the capacity of UV-CE as a complimentary technique to further understand the aggregation process.