Post-weaning multi-systemic wasting syndrome (PMWS), which is primarily caused by porcine circovirus type 2 (PCV2), is an emerging swine immunosuppressive disease. To characterize the interaction between target immune cells and PCV2, the differential proteomes of porcine alveolar macrophages, with and without PCV2 infection, were analyzed at different time points with two-dimensional gel electrophoresis (2-DE) followed by MALDI-TOF/TOF identification. Mass spectrometry identified 21 altered host-encoded protein spots (9 up-regulated and 12 down-regulated protein spots), which included cytoskeleton proteins, macromolecular biosynthesis-associated proteins, stress response proteins, signal transduction proteins, energy metabolism, and ubiquitin proteasome pathway-associated proteins. The majority of the changes occurred 48h after PCV2 infection. Moreover, 9 corresponding genes of the differentially expressed proteins were quantified by real time RT-PCR to examine the transcriptional profiles. Western blot analysis further confirmed the differential expression of proteins, including SFN, PSME1, PRP19, HSPB1, TUBA|B, CK-19 and ACTB, in the proteomic profiles. Subcellular distribution analysis of the cytoskeletal proteins and PCV2 clearly demonstrated interactions between PCV2 and the differential protein β-tubulin. Thus, this work effectively provides useful and dynamic protein-related information to further understand the underlying pathogenesis of PCV2 infection.