Finding the optimal recombinant adeno-associated virus (rAAV) serotypes for efficient as well as tissue specific transduction has become imperative for successful gene therapy. We used rat condylar chondrocytes, osteoblast-like cell line UMR106 and bone marrow stromal cells (BMSCs) to evaluate the transduction efficiency of different rAAV serotypes in vitro; hoping to establish an efficient in vivo rAAV mediated delivery system for gene therapy in craniofacial region. All of the selected rAAV serotypes were able to infect target cells and gave rise to eGFP expression and VEGF secretion. Quantified by fluorescence activated cell sorter (FACS) and ELISA analysis, rAAV2 was superior for efficient transduction of rat chondrocytes, rAAV1 was most efficient when introduced into UMR 106 cell line and rAAV5 yielded the highest infection efficiency in BMSCs. Hence, differences in receptor binding in different oral tissues and transduction pathways suggest rAAV based hybrids have various transduction efficiencies and can efficiently target different oral tissues.