Differential in-gel electrophoresis showed contrasting effects of the transgenic expression of an alpha-amylase inhibitor from beans on the proteomes of two pea cultivars. One cultivar showed minor changes relative to its non-transgenic parent with only one protein changing by more than about twofold. Changes in the abundance of certain endogenous proteins in the other cultivar were of greater number and magnitude with some endogenous proteins undetected while some new protein spots appeared in the transgenic proteome. The sets of proteins with altered expression were generally different between the two cultivars. Some of the proteins that were differentially expressed were identified by MS. Most were seed storage globulins, which are sited together with the transgenic product. Some of the changes may be due to alterations in expression levels but there were also changes due to post-translational processing.