Fluid-induced shear stress is widely recognized as an important biophysical signal in cell-cell mechanotransduction. To identify cellular signaling pathways that are regulated by fluid shear stress, we applied the unbiased approach of transcriptional profiling. Our cDNA array analysis detected that 1,165 of the 6,288 sampled unigenes were significantly affected by pulsatile fluid flow. GenMapp 2.1 analysis revealed pathways of genes regulated by shear stress: angiogenesis, blood vessel morphogenesis, regulation of endothelial cell proliferation, and prostaglandin biosynthesis. Individual genes significantly up-/downregulated by shear stress included vascular endothelial growth factor A (Vegf a), cysteine-rich protein 61 (Cyr61), platelet-derived growth factor-alpha (Pdgf a), connective tissue growth factor (Ctgf), Neuropilin 1 (Nrp1), angiotensin II receptor, type 1 a (Agtr1 a) and fibroblast growth factor 1 (Fgf1). Based on these findings, we hypothesize that fluid shear stress-regulated Vegf most likely stimulates MC3T3-E1 cells through autocrine/paracrine release and may provide a powerful recruitment signal for osteoclasts, endothelial cells, and/or stem cells during bone remodeling.