Publisher Summary This chapter describes various techniques used in the whole chromosome analysis. Whole chromosomes can be studied in a variety of ways, both physically and genetically. The advent of pulsed-field gel electrophoresis (PFGE) technology has made it possible to study whole genomes physically in ways not possible before. The methods described in the chapter can be applied to artificial and foreign chromosomes, as well as to the native chromosomes of S. cerevisiae. The chapter gives examples of the techniques that anyone can use, as well as some that require specialized equipment. This includes PFGE techniques for electrophoretic karyotyping for species identification and chromosome evolution, for aneuploid detection and other chromosome abnormalities, and for physical mapping of meiotic double-strand break (DSBs). Other techniques include genetic marking of difficult regions for physical and genetic mapping, whole chromosome transfers for functional and compatibility studies, and the analysis of chromosomal alterations for the search of new functional elements. The more difficult techniques are the analysis of the sublocalization of chromosomal elements within the nucleus using fluorescent in situ hybridization (FISH) and immunofluorescence (IF).