Introduction: Diseased Piper nigrum plants have affected pepper berry production in Sarawak farms, contributing to the economic loss for farmers that depend on this species for their income. Objective: This study was performed to analyse the protein profiles of healthy and diseased P. nigrum roots and to identify differentially expressed proteins. Methods: Two methods of protein extraction were compared, and the extracted proteins were quantified through two quantitative assays: the Bradford and BCA assays. The Phenol/SDS extraction method was significantly better compared to the phenol method. Results: The SDS-PAGE analysis revealed two differently expressed unique proteins bands with the molecular size of approximately 20 kDa and 12.5 kDa present in the sample of diseased plants. These differentially expressed proteins are likely to be pathogenesis-related (PR) proteins which are produced as a response to infection. Conclusion: These PR proteins can potentially be used as markers or be developed further to allow plants to gain systemic resistance against diseases.