This study was designed to compare the temporal changes of gene expression profile in osteoblastic cell lines (SaOS-2) treated with low-intensity pulsed ultrasound stimulation (LIPUS) using complementary DNA (cDNA) microarrays. SaOS-2 cells were treated with LIPUS for 20min. Thereafter, cells were harvested and RNA was extracted twice at 4 and 24h, respectively. Using cDNA microarrays, 7488 genes with changes in expression in SaOS-2 cells were identified for comparison. Microarray analysis revealed a total of 165 genes in SaOS-2 cells were regulated at 4 and 24h after LIPUS treatment. Except for 30 known LIPUS-regulated genes, our study demonstrated for the first time that over 100 genes were related to the underlying molecular mechanism of LIPUS and suggested that LIPUS might regulate a transient expression of numerous critical genes in osteoblastic cells. These results provide further understanding of the role of LIPUS in the regulation of osteoblastic gene expression potentially involved in the molecular mechanism of osteogenesis in fracture repair.