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Numerous machine elements are operated in mixed lubrication regime where is governed by a combination of boundary and fluid film effects. The direct contact between two surfaces reduces a machines life by increasing local pressure. In order to estimate machine's life exactly, the effect of asperity contact should be considered in the lubrication model. In this study, new 3-dimensional partial elasto-hydrodynamic lubrication (PEHL) algorithm is developed. The algorithm contains the procedures to find out solid contact regions within the lubricated regime and to calculate both the pressure by fluid film and the contact pressure between the asperities of the solids. Using the algorithm, we conducted the PEHL analysis for the contact between the rotating shaft and the inside of pinion gear. To investigate the effect of surface topology two different surfaces with sinusoidal profile are used. Both film thickness and pressure are calculated successfully through the PEHL algorithm.