The effects of specific mechanical energy (SME) on soy protein aggregation during extrusion process were studied using a combination of size exclusion chromatography, multi-angle laser light scattering (SEC-MALLS) and dynamic light scattering. Results showed that the weight-average molecular weights (M-w) of soy protein isolate (SPI) and those of the aggregates increased 74-104% and 39-67%, respectively after the extrusion treatments. However, they decreased from 2.688 to 2.340 x 10(6) g/mol and from 1.115 to 0.926 x 10(7) g/mol, respectively when SME increased from 839.81 to 1277.01 kJ/kg. The increasing SME caused the proportion increase of low molecular weight fractions from 35.02% to 52.63% as well. It was concluded that protein was disassociated/depolymerized by mechanical shear during the extrusion process, and the increasing SME could enhance the extent of breakdown of protein aggregates. There existed vital factors contributing to the aggregation of proteins, and more information of the vital factors needs to be further investigated. (C) 2012 Elsevier Ltd. All rights reserved.