The described integrated sexual assault analysis workflow uses multiple STR systems. Selection of the appropriate system is based on the results of the sample assessment. A robust standard autonomic STR system is an integral part of the sexual assault analysis workflow. The high discriminatory power and compatibility with criminal DNA databases makes a standard autonomic STR system the optimal typing system for most sexual assault evidence; however, certain complex mixtures or other challenging samples may require an alternative STR system in order to obtain useful results. For evidence that contains a trace amount of male DNA present in a large background of female DNA, a Y-chromosome specific STR system may be the best method for obtaining conclusive or probative results. Because of the inherent male specificity of Y-STRs, a minor male component of a mixture, which can be undetected by standard autonomic STR analysis, can often be detected with a Y-STR system without any interference from the larger female contributor. The resulting Y-STR haplotype can be easily used to include a suspect who has been identified by investigators, or to exclude a suspect from further investigation. The two case scenarios presented in this article illustrate a new way of processing biological samples and the importance of enhancing the data assessment capabilities of sexual assault evidence and other samples. With the advent of new technologies, laboratories can evaluate their existing procedures and develop the most efficient system that produces the most probative results. The revised process can be integrated into existing workflows. 2 figures and 3 references