Linkage analysis is a statistical genetics method to localize disease and trait genes to specific chromosome regions. The analysis requires pedigrees with members who vary among each other in the trait of interest and who have been genotyped with known genetic markers. Linkage analysis tests whether any of the marker alleles cosegregate with the disease or trait within the pedigree. Evidence of cosegregation is then combined across the families. We describe here the background and methods to conduct a linkage analysis for a binary trait, such as a disease, when the model of the gene contributing to the trait can be formulated. There are a number of statistical genetics software packages that allow you conduct a model-based linkage analysis of a binary trait. We describe in great detail how to run one of the programs, the LODLINK program of the Statistical Analysis for Genetic Epidemiology (S.A.G.E.) package. We provide directions for making the four input files and information on how to access and interpret the output files. We then discuss more complex analyses that can be conducted. We discuss the MLOD program for multipoint linkage analysis, including its relation to LODLINK and the additional file needed. Notes to improve your ability to run the program are included.