Fluid shear stress (FSS) is a potent physical cell signal in the regulation of bone remodeling. Although the effects of FSS on bone cells of the osteoblastic lineage have been studied extensively, less is known about the direct effect of FSS on osteoclasts. In this study, we investigated the direct influence of FSS on rat osteoclasts isolated by a classic mechanical anatomical technique. Osteoclasts were exposed to an FSS of 2.9 dynes/cm2 for a given period, or subjected to various magnitudes of FSS for 30 min. Cell morphology under FSS was observed and the expression of the mRNA of ATP6V1A and TCIRG1, two crucial subunits of the vacuolar H+-ATPase gene, was analyzed by quantitative real-time PCR. Changes in osteoclast morphology were apparent after the application of FSS, including increased cell volume, strengthened refraction and decreased transmittance. Time-dependent and dose-dependent increases in ATP6V1A and TCIRG1 mRNA expression were seen in response to FSS within 30 min. However, a duration of FSS exceeding 30 min induced a significant decrease in ATP6V1A and TCIRG1 mRNA expression. FSS therefore appears to be a potent stimulus that is sensed by rat osteoclasts and results in significant changes in cell morphology and the gene regulation of ATP6V1A and TCIRG1. These effects might be strictly dependent on the duration of FSS.