This study characterizes 3 cases of mesenchymal chondrosarcoma (MC) utilizing a proteomic approach that allows for the detection, visual quantification, cellular compartmentalization, and assessment of the functional state of certain proteins that may promote tumor growth and/or oppose apoptosis. Immunohistochemical procedures were performed to detect the following protein antigens: CD99, interleukin (IL)-1α, IL-6, transforming growth factor (TGF)-α, conventional (c) protein kinase C (cPKC)-α, cPKC-βII, phosphorylated (p)-PKC-α/βII, c-kit (CD117), platelet-derived growth factor receptor (PDGFR)-α, PDGFR-β, epidermal growth factor receptor (EGFR), human epidermal growth factor receptor (HER)-2/neu, cathepsin D, angiotensin-converting enzyme (ACE), angiotensin II type 1 (AT1) receptor, p21ras, the α subunit of farnesyl and geranylgeranyl transferase (FTα/GGTα), phospho (p)-c-Jun N-terminal kinase (p-JNK), p-p38 mitogen-activated protein kinase (MAPK), cyclin D1, c-Jun, Ki-67, bc1-2, TGF-β1 latency-associated peptide (LAP), TGF-βRII, and cyclooxygenase (COX)-2. Immunoreactivities were scored from 0 to 3+ positivity using bright-field microscopy. The results showed that malignant mesenchymal chondroblasts exhibit stronger expressions of CD99, IL-1α, cPKC-α, p-PKC-α/βII, PDGFR-α, p-JNK, Ki-67, and bc1-2 antigens than their more mature-appearing chondrocytic counterparts in MC. In conclusion, molecular profiling of mesenchymal chondrosarcoma using a proteomic approach characterized the mesenchymal chondroblasts as possessing pathways that incorporate PKC-α and PDGFR-α signaling and anti-apoptotic bc1-2 expression. Specific therapies to target the mesenchymal chondroblasts in mesenchymal chondrosarcoma might include interferon-α, rapamycin, ciprofloxacin, and STI571.