Flank modifications are often made to overcome the influences of errors coming from manufacturing and assembly processes, as well as deflections of the system. This paper presents a semi-analytical approach on estimating the axle system deflections by combining computer simulations and actual loaded contact patterns obtained from lab tests. By using an example hypoid gear design, influences of axle deflections and typical flank modifications (lengthwise crowning, profile crowning and twist) on stress distribution of the hypoid gear drive are simulated. Finally, several experimental gear samples are made and tested. Tooth surface topography is examined by using a Coordinate Measuring Machine. Test results are reported to illustrate the effect of tooth flank modifications on contact fatigue life cycles.