As a result of the complex blood flow patterns that occur in the arterial tree, certain regions of the vessel wall experience fluctuations in shear stress that are dominated by harmonic frequencies higher than the heart rate (11). To assess whether variations in frequency affect endothelial gene expression, the gene expression patterns of cultured porcine aortic endothelium exposed to three sinusoidal waveforms (1, 2, and 3 Hz; amplitude = 15 dyn/cm²) and one physiological waveform were compared to the expression profiles elicited by steady flow. At each frequency, including steady flow, three levels of mean shear stress (0, 7.5, and 15 dyn/cm²) were used. Following 24 h shear exposure, RNA was extracted for microarray analysis against 10,665 Sus scrofa oligonucleotides. A two-way ANOVA identified 232 genes whose transcription was differentially modulated by frequency, while mean shear significantly affected the expression of ~3,000 genes. One-way ANOVAs showed that the number of frequency-dependent genes increased as the mean shear stress was reduced. At 1 Hz, several inflammatory transcripts were repressed relative to steady flow, including VCAM and IL-8, while several atheroprotective transcripts were induced. The antiinflammatory response at 1 Hz was reversed at 2 Hz. The proinflammatory response evoked by the higher frequency was most pronounced under reversing and oscillatory shear. This study suggests that arterial regions subject to both shear reversal and dominant frequencies that exceed the normal heart rate are at greater risk for atherosclerotic lesion development.