Fuel filters used to remove particulates from liquids are evaluated by OEM’s and filter manufacturers using standardized test protocols that specify simplified conditions that aid in laboratory reproducibility. These test results do not always translate into actual filter performance in application. In military vehicles that experience frequent demands for rapid acceleration and deceleration and extreme vibration, the importance of evaluating fluid filtration performance with these parameters as inputs is significant. This paper discusses an investigation of the performance sensitivity of a diesel particulate filter to structural vibration properties and flow rate fluctuation. After determination of this sensitivity to dynamic inputs, a new test protocol was developed for evaluating competitive fuel filters. The cyclic flow and mechanical vibration inputs for the new protocol were selected to be representative of those that would be seen in a heavy duty diesel application. Finally, six competitive heavy duty diesel filter models were compared using a traditional filter efficiency measurement procedure and the newly developed protocol. The performance of the competitive filters using the traditional protocol suggested that most of the filters were nearly identical, whereas the new protocol yielded performance differences that demonstrated clear advantages of specific filters in terms of filter efficiency under dynamic conditions.