Castor bean (Ricinus communis L.) seeds serve as raw material for the production of nonedible oil used in medicine and industry, whereas the presence of allergenic and toxic proteins in the residue left after oil extraction precludes the use of this protein-rich by-product in animal feeding. To better understand the enzymes involved in the biosynthesis and degradation of fatty acids and to identify proteins with toxic/anti-nutritional properties, extracts of developing and germinating seeds were prepared and prefractionated according to solubility properties of the proteins. An enriched plastid organelle fraction embracing mostly plastids and mitochondria was also prepared. Two-dimensional electrophoresis (2DE) reference maps of these fractions were obtained from which nearly 400 proteins were identified by matrix-assisted laser desorption ionization-time of flight-time of flight (MALDI-TOF-TOF) mass spectrometry after a search in a National Center for Biotechnology Information (NCBI) database and in an expressed sequence tag (EST) primary bank prepared from a cDNA library of developing seeds. These proteomics techniques resulted in the identification of several classes of seed reserve proteins such as 2S albumins, legumin-like and seed storage proteins, as well as other proteins of plastidial or mitochondrial functions and proteins involved in plant defense against biotic and abiotic stresses. It is expected that the collected data will facilitate the application of genetic techniques to improve the quality/profile of castor seed fatty acids, and pave the way for a rational approach to inactivate allergenic and toxic proteins, allowing the use of castor bean meal in animal feeding.