Cryptorchidism (CO) is an urogenital anomaly, in which the testis does not descend through the inguinal canal into the scrotum and occurs in human, as well as in other mammalian species. It is associated with a higher probability of infertility and tumors. Most of the studies so far have been focused on identification of single loci genetic causes, while less attention has been paid to data editing and bioinformatics analyses for identification of reliable candidate biomarkers. The masters thesis contains three chapters; update of the database of CO loci, bioinformatics, and experimental analysis. The database consists of 487 loci from eight species, sorted according to the clinical biotype of CO. We have developed a standardized form for reporting of human loci associated with CO in the scientific literature. We performed three bioinformatics analyses. We have identified 18 smallest regions of overlap (SROs), that consist of 927 genes, including 60 human CO genes, and four in other species. We developed a new study approach, named genome wide screening for SROs; GW-SROs. In the pathway enrichment analysis using the DAVID tool we identified 63 significant pathways associated with 281 CO genes in human. In the protein interaction analysis using the STRING tool we identified five modules. Four genes which are present in the results of all three bioinformatics analyses can be considered as reliable candidates for CO. Using the aCGH method we identified 23 copy number variants (CNV) in the slovene population of patients with CO and/or infertility. In the masters thesis we have analysed genotype-CO associations using several approaches and prioritized candidate biomarkers for CO. Results of this study present a basis for further narrowing of SROs, identification of new candidate functional modules for CO, and their experimental validation in human and other mammalian species.