Coffee is one of the most valuable agricultural commodities. There is much agronomic research on coffee, but molecular knowledge of its fruit development and ripening is limited. This study reports a comparative proteomic investigation of immature coffee fruits in two early developmental stages: stage 1, cell division and elongation of the perisperm; and stage 2, early growth of the endosperm progressively replacing the perisperm. Proteins were extracted using a modified SDS-phenol method and two-dimensional electrophoresis gels stained with Coomassie blue revealed about 300 well-resolved polypeptide spots in the pH range of 3 to 10. The differentially expressed polypeptides spots were excised, trypsin-digested, and analyzed by MALDI-TOF mass spectrometry. Peptide MS data were searched against the coffee EST database. Most of the identified protein spots are involved in the glycolytic pathway and energy reserve, and are more highly expressed at stage 2.