A short account of the development of classical genome analysis, the analysis of chromosome behaviour in metaphase I of meiosis, primarily in interspecific hybrids, is given. The application of the concept of homology to describe chromosome pairing between the respective chromosomes of a pair during meiosis is traced, and the relationship between this use of homology and the concept of homology as common ancestry is discussed at length. To equate the two concepts has led to the erroneous assumption that levels of chromosome pairing is an indication of phylogenetic relationship. Even accepting the fundamental premises, genome analysis is burdened by observational difficulties. Hence, chromosome pairing has been shown to be under genetic control and is also influenced by environmental conditions. Additionally, basic biological observations such as the distribution of meiotic configurations or the identity of the individual chromosomes are frequently neglected. Data from chromosome pairing are captured as pair-wise comparisons and are amenable only to phenetic analysis, and hence are not suited for phylogenetic inferences. As currently perceived, genome analysis may have a role to play in plant breeding but it has no place in systematics. With an increased knowledge and understanding of the mechanism behind meiosis, data useful in a systematic context may eventually be produced.