Citrus sudden death (CSD) is a disease of unknown etiology affecting citrus trees. It affects sweet orange and mandarin tress grafted on Rangpur lime or Volkamer lemon rootstock. Recent figures account the death or erradication of 4 million trees due to CSD. To date, no pathogen was confirmed as the etiological agent of this disease. We took advantage of a proteomic approach, employing bidimensional electrophoresis followed by protein identification by mass spectrometry, to identify proteins differentialy expressed in CSD-affected trees. CSD is characterized by a graft union incompatibility, where an intense phloem multiplication occurs, turning bark from white to yellow. Currently, this yellow discoloration is the only judgement for a doubtful symptomatic canopy. Our purpose is to compare healthy and diseased rootstock bark tissue proteins, identifying changes in protein expression as a tool to search for CSD biomarkers. We developed an effective protocol, employing denaturing primary extraction, precipitation with acetone and ressuspension in buffered urea/thiourea/CHAPS/Triton X-100. Isoelectric focusing was carried out with IPGStrips and second dimension in Tris-Glycine gels. Proteins were stained with colloidal coomassie blue and spots were cut, digested with trypsin and subjected to mass spectrometry analysis (Maldi-ToF-Tof). Searches were done with PMF and MS/MS profiles using Mascot (MatrixScience). Previously we have identified proteins present in healthy bark that are down-expressed in CSD-affected bark. Here, besides making an comprehensive comparison of healthy and CSD-affected protein profiles, we show that this profile is a predictive way to monitor cannopy symptom appearance. Besides shedding some light in the biochemistry of the disease, our aim is to develop a diagnosis test based on the absence or presence of specific proteins, making precocious CSD diagnosis possible.