Vascular endothelial cells (ECs) play significant roles in regulating circulatory homeostasis. The shear stress resulting from circulatory flow modulates EC functions by activating mechano-sensors, signaling pathways, and gene and protein expressions. Sustained shear stress with a clear direction (e.g., the pulsatile shear stress, PS, in the straight part of the arterial tree) down-regulates the molecular signaling of pro-inflammatory and proliferative pathways. In contrast, shear stress without a definitive direction (e.g., the disturbed or oscillatory flow, OS, at branch points and other regions of complex geometry) causes sustained molecular signaling of pro-inflammatory and proliferative pathways. The EC responses to directed mechanical stimuli involve the remodeling of EC structure to minimize alterations in intracellular stress/strain and elicit adaptive changes in EC signaling in the face of sustained stimuli; these cellular events constitute a feedback control mechanism to maintain vascular homeostasis and are athero-protective. Such a feedback mechanism does not operate effectively in regions of complex geometry, where the mechanical stimuli do not have clear directions, thus placing these areas at risk for atherogenesis. The differential modulation of EC functions by various flow patterns involves intricate interplays of signaling pathways and gene regulation, with the participation of microRNA (miR). For example, miR-23b mediates the PS-induced inhibition of EC proliferation by causing RB hypophosphorylation, and miR-21 mediates the OS-induced monocyte adhesion to ECs by enhancing the expression of adhesion molecules such as vascular cell adhesion molecule-1 and monocyte chemotactic protein-1. miR-92a exerts an inhibitory effect on the transcription factor KLF2, which is anti-inflammatory and anti-proliferative. The athero-protective effect of PS is mediated by the inhibition of miR-92a and the atherogenic effect of OS is mediated by the activation of miR-92a. There is also evidence that ECs can release miR-126 to modulate the gene expression and functions of vascular smooth muscle cells via a paracrine mechanism. These experimental studies on miR, in combination with the in silico approaches in systems biology, provide new insights on the mechanism of the fine tuning of gene regulation in response to differential flow patterns in health and disease.