Copy number variation (CNV) is a variation of large fragment deletions, duplications, insertions and complex multi-loci polymorphism in genome. This variation may cause a change in gene numbers or chromosome abnormalities, and that may lead to disease, like schizophrenia and autism, and may even be related to the generation of tumor and tumor susceptibility. Cancer is the most prevalent diseases worldwide. Therefore, this thesis analyzes and discusses the correlation between the tumor and CNV. We have performed the disease-related CNV analysis using in Affymetrix Human SNP array 6.0, that have investigated blood samples and tumor samples of the head and neck squamous cell carcinoma (HNSCC) from Changhua Christian Hospital and Chang Gung Memorial Hospital in Taiwan respectively. Our aim is to understand HNSCC from a genetic and prognostic point of view and find a disease-specific performance in Taiwanese people.