The Human Genome Project is providing life science researchers with access to unprecedented amounts of raw sequence data. To effectively harness this data and apply it to biomedical research, therapeutic development, clinical practice and patient management, powerful new tools for measuring gene expression, polymorphism discovery and genotyping are needed. GeneChip probe arrays are powerful tools to meet these requirements. Light-directed chemical synthesis is used to generate miniaturized, high-density arrays of oligonucleotide probes called GeneChip probe arrays. Application-specific oligonucleotide arrays have been used to rapidly scan known genes and discover genetic variants, to detect the presence of known alternative alleles and to simultaneously measure the expression of thousands of individual genes. An integrated GeneChip system including instrumentation and software has been developed for array hybridization, fluorescent detection, and data acquisition and analysis. Experiments demonstrating the effectiveness of these methods of genetic analysis will be decribed.