Endothelial cells elongate and align with the direction of applied fluid shear stress. Previously, automated methods for analysis of cell orientation distribution have used Fourier- or fractal-based methods. We used intensity gradients in images of control and sheared endothelial cells to measure orientation distributions. Automated measurements of mean orientation and angular deviation compared favorably with manual measurements. There was a significantly greater angular deviation in images of control cells compared with sheared cells. Automated methods were also used to quantify organization of cytoskeletal fibers using the local angular deviation and a measure of the local coalignment of fibers called the coalignment ratio. The local angular deviation of microtubules and microfilaments was significantly smaller in sheared cells compared with control. The coalignment of cytoskeletal fibers was significantly greater in sheared cells. We conclude that image intensity gradients can be used rapidly, accurately, and objectively to measure cell orientation distributions and cytoskeletal filament organization.