Many recent studies have indicated that virus-like particles (VLPs) have many potential applications in the fields of vaccine development and gene therapy. However, we still know little about the subtle mechanisms involved in the presentation of VLPs by antigen presenting cells (APCs). To illustrate the mechanisms, we utilized two-dimensional electrophoresis and tandem MS to compare and identify differentially expressed proteins between hepatitis B virus core antigen VLP (HBc-VLP)-pulsed and control RAW264.7 cells. Of the 25 spots identified as differentially expressed ( p < 0.05) between the two cell lines, 11 (corresponding to 11 unique proteins) were positively identified. Further analysis of two proteins, prohibitin and heat shock protein 70, confirmed that these proteins are expressed at higher levels in HBc-VLP-pulsed RAW264.7 cells compared with control cells. The proteins identified in this study will be useful in revealing the mechanisms that underlie VLP-APC interactions. Overall, this study also provides some useful suggestions for vaccine development and gene therapy.