||The molecular genetic characterization of the diversity present in the CIMMYT maize and wheat germplasm collections is an ongoing process, to which many different persons have contributed. Furthermore, one of the mandates of CIMMYT is training of our national program partners, who have also expressed interest in learning the statistical techniques we use here at CIMMYT. It may even be possible one day to combine data from different labs into one analysis. In an effort to standardize the process and the results, and as a teaching tool for interested parties, this manual was prepared to act as a set of guidelines for future diversity analyses of maize and wheat germplasm. The analysis tools will also work in other species. Three main steps are involved in the statistical analysis of molecular data in diversity studies: (1) Data collection (scoring and entry of band information into the computer); (2) Data analysis using Univariate and Multivariate Statistical approaches; and (3) Interpretation of the data. Each tep in the process should follow a standardized format if the output of one diversity study is to be compared to other studies and inferences drawn in this manner. Likewise, laboratory procedures must be standardized between different workers; to achieve this end, all users should read the manual entitled “Laboratory Protocols: CIMMYT Applied Molecular Genetics Laboratory,” which should be followed when initiating diversity studies. This manual will provide both simple examples of all procedures in the main body of the text and real examples of data analyses in the appendices. Please refer to these examples when questions arise regarding any procedure mentioned in this manual.