Mu-HPLC has previously been used to increase the resolution and sensitivity of protein separations but never for the analysis of soybean proteins. In this work, soybean proteins were, for the first time, separated using a capillary column with an internal diameter of 150 microm packed with a Genesis C18 stationary phase (4 microm, 300 angstroms) and UV detection. TFA and acetic acid were investigated as ion-pairing reagents in order to optimise water-ACN gradients to achieve this separation. The column showed good selectivity enabling the separation of soybean proteins from other vegetable proteins such as cereal (wheat, rice and corn) and also from milk proteins. The developed method was applied to the detection of soybean proteins in commercial products elaborated with mixtures of vegetable proteins.