Basal stem rot disease in oil palm is caused by the fungus, Ganoderma boninense. Proteomics approaches using two-dimensional gel electrophoresis (2-DE) were adopted to identify proteins from oil palm that were differentially expressed in response to the fungus. Total proteins were extracted from oil palm roots after Day 3 and Day 7 post-infection and resolved in 2-DE gels. Differentially expressed protein spots between the infected and uninfected palms were determined using PD-Quest Software. Seven protein spots were differentially expressed in the infected root at Day 3 post-infection. At Day 7, the number of differentially expressed protein spots increased to 25, with a molecular weight less than 50 kDa. All protein spots were analysed by MALDI TOF/TOF mass spectrometry. Twelve candidate proteins were identified by a comparison of differentially expressed proteins at Day 7 with the database. One of the candidate proteins is glucanase, which is widely known to induce during fungal response in other plants. Other candidate proteins that were identified were also involved in defence and stress responses in other plants, suggesting that these proteins play a significant role in oil palm root pathogenicity response towards G. boninense infection