Complex traits are multifactorial traits controlled by polygenic host factors. These trait-related phenotypic characteristics and performance including body weight, blood chemistry, immune cell profiles, as well host susceptibility to infectious and chronic diseases. In recent years, tremendous efforts were invested aiming to map the host genetic factors attribute to these traits and subsequently clone the gene/s underlying these loci. In parallel to human studies, a number of mouse models and approaches were developed aimed to enhance the mapping process and the gene cloning. These include of using resources such as F2, backcross, advanced intercross lines, outbred populations, consomic, congenic and recombinant inbred lines (RIL). The constraints of these approaches were the limited resolution mapping of genomic regions of the quantitative trait loci (QTL) associated with the trait of interests, and the limited genetic diversity observed in the parental founders. To overcome these limitations, a new genetically highly diverse recombinant inbred lines of mouse population was established, namely the Collaborative Cross (CC), created from full reciprocal mating of 8 divergent strains of mice:A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, NZO/HiLtJ, CAST/Ei, PWK/PhJ, and WSB/EiJ. By intercrossing these eight founders to generate the different CC lines, the genetic makeup of the newly developed resource is completely different from the eight parental lines, and will show heterosis, which subsequently will response differently comparing with their original founders. Finally, our results suggest that it is not essential to defining the phenotypic response of the eight parental lines, prior of assessing the CC lines, because it is believed that genetic interaction of the new genetic makeup of the new lines will reveal new phenotypic response, which completely different from the parental lines.In this report, we present to the community the power of the CC for dissecting variety of complex traits including host susceptibility to infectious and chronic diseases as well body performance traits. Based on our results from a variety of studies, we recommend to the community, that the best strategy of using this population is to aim of phenotyping about 50 and more of CC lines, with limited number of biological replicates (3-4 mice per line), and subsequently using the publicly available high dense genotype information of the CC lines as well the sequence database of the eight founders, it will be possible performing QTL mapping to a unprecedented precision genomic regions less than 1 MB, subsequently lead to identify potential strong candidate genes. These achievements are believed cannot be obtained with any other currently available mouse resource populations.