Basic principles and methods of genetic analysis were covered in this chapter. The approaches of linkage analysis for Mendelian or complex disorders can be summarized in the following flowchart (Fig. 2). It is important that the clinical, analytical, and molecular investigators be involved in all steps in the process. Mapping genes for complex disorders is often more difficult than mapping genes for Mendelian disorders, but both may prove to be very important in understanding disease processes and designing new treatments. Practical use of computer programs available for genetic analysis is detailed elsewhere (24).