Cowpea (Vigna unguiculata) seeds are a major source of dietary protein for low income families in northeastern states of Brazil.  As the proteins in the seeds are deficient in sulfur-containing amino acids, increasing the level of these amino acids in seeds is a major goal of both classic and gene-transfer based methods of genetic improvement of this legume species. We are interested in determining the patterns of protein deposition in developing zygotic and somatic embryos. Our aim is to identify genes with specific patterns of expression during embryogenesis, so that they can be used in programs for the genetic improvement of cowpea. Using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) we compared the protein patterns of developing seeds of cowpea at 8, 10 and 18-days after anthesis (DAF). For each developmental stage we obtained around 400 protein spots that were highly reproducible across an isoelectric focusing range 3-10. The protein profile of several spots differed significantly between the three conditions; based on spot quantity and quality, and the expression rate in the three conditions, 77 protein spots (up-regulated or down-regulated during development) were selected for tandem mass spectrometry analysis. The peptide sequences were identified by database searching of uninterpreted fragment ion mass spectra with the PEAKS software, against an EST database containing DNA sequences of approximately 550,000 ESTs of seven species of the Fabaceae Family and the NCBI database. This resulted in the identification of 40 proteins, some of which have not been previously detected in cowpea seeds. Most of these were identified as reserve proteins, defence proteins or late embryogenesis abundant (LEA) proteins.