Genomewide association studies (GWAS) have been widely used in recent years to identify common variants that are associated with multiple types of cancer, including testicular germ cell tumors. These studies require no a priori hypotheses and have advantages, including the ability to highlight new pathways relevant to the biology of common diseases. GWAS require collection of germline DNA from individuals with and without the disease of interest. Following DNA extraction and quantification, a variety of array based platforms are available to evaluate common and moderately rare germline variation throughout the genome in an agnostic fashion. Here, we describe DNA extraction methods from samples typically used in the evaluation of germline genetic variation (blood and saliva). We also describe assays used to assess DNA quality and quantity. Finally, we include methods describing array based genotyping using the Illumina platform and validation of relevant variants using the iPLEX Agena Multiplexed Genotyping (formerly Sequenom).