During the last decades a decline in male reproductive health has been observed in Nordic countries, and particularly in Denmark. Testicular cancer is the most fatal form of male reproductive disorders, and despite high remission rates it is typically accompanied with infertility. The main topic of this thesis is the identification of the molecular basis of male reproductive disorders, with a special focus on testicular cancer. To this end, clinical samples were characterized by microarraybased transcription and genomic variation assays and molecular entities were identified by computational analysis of such data in conjunction with data from publicly available repositories. This thesis presents an introduction to disease genetics and molecular systems biology, followed by four studies that each provide detailed clues to the etiology of male reproductive disorders. Finally, a fifth study illustrates the use of massively parallel nucleotide sequencing for gene expression analysis. In paper I the similarity of testicular carcinoma in situ cells from the developing testis was investigated. We observed a close similarity to gonocytes, contributing further indications that non-spermatocytic testicular cancer arise due to disturbances in early testicular development. In paper II we analysed copy number variations (CNV) in germline DNA from four families with testicular germ cell tumors. Given the low number of samples, we aimed to improve the confidence by placing CNVs in a protein network context superimposed with established phenomic information. We thereby identified a recurrent CNV at a locus with genes encoding for the relaxin peptide hormones, indicating their potential role in testis function. Paper III presents a genome-wide assocation study on testicular dysgenesis syndrome. We confirmed the importance of KITLG in testicular cancer, and identified two risk loci related to the TGF ß-signaling pathway, TGFBR3 and BMP7, by using a systems biology approach that was guided by the developmental disease hypothesis, and a pathway analysis based approach, respectively. Paper IV investigate the genome-wide association data with respect to copy number variation and show that the aggregated effect of rare variants can influence the risk for testicular cancer. Paper V provides an example of the application of RNA-Seq for expression analysis of a species with an unsequenced genome. We analysed the plant Craterostigma plantagineum, which is known for its astonishing drought tolerance, and thereby provided the first transcriptomes of this species. Comparisons of unstressed to desiccated conditions indicated several pathways of interest. In conclusion, this thesis contributes to the molecular understanding of testicular malfunction and desiccation tolerance in C. plantagineum, as well as develops and highlights the usefulness of novel systems biology methodologies.