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Homologous chromosomes are chromosomes in a biological cell that pair (synapse) during meiosis, or alternatively, non-identical chromosomes that contain information for the same biological features and contain the same genes at the same loci but possibly different genetic information, called alleles, at those genes. For example, two chromosomes may have genes encoding eye color, but one may code for brown eyes, the other for blue.

Non-homologous chromosomes representing all the biological features of an organism form a set, and the number of sets in a cell is called ploidy. In diploid organisms (most plants and animals), each homologous chromosome is inherited from a different parent. But polyploid organisms have more than two homologous chromosomes.

Homologous chromosomes are similar in length, except for sex chromosomes in several taxa, where the X chromosome is considerably larger than the Y chromosome. These chromosomes share only small regions of homology.

Humans have 22 pairs of homologous non-sex chromosomes (called autosomes). Each member of a pair is inherited from one of their two parents. In addition, female humans have a homologous pair of sex chromosomes (2 X's); males have an X and a Y chromosome.

The definition of homologous chromosomes is difficult, and all commonly used definitions have problems. The first definition given above is the standard cytological definition. According to it, homologous chromosomes are pulled together during prophase I of meiosis, by the synaptonemal complex. It implies that X and Y chromosomes are homologous. The problem is that it says that in amphidiploids, each chromosome has x homologues (the number of chromosomes in a gamete), instead of the expected n.

The second definition is the molecular genetics definition. It gives the expected number n for amphidiploids, but implies that X and Y are not homologous, which makes ploidy difficult to define.

Homologous chromosomes are not to be confused with sister chromatids, the identical chromosomes that separate during mitosis or meiosis II.

Homology of chromosomes is different than homology of genetic sequences, and predates that use of the term homology. An exception arises with allopolyploidy where chromosomes pair up by age, so sequence similarity is used to determine the original chromosomal sets.

Homologous chromosomes are also very similar to, and often confused with the term synteny (or gene homology)—which refers to genes located on the same chromosome.

• Comparative Maps NIH's National Library of Medicine NCBI link to Gene Homology resources, and Comparative Chromosome Maps of the Human, Mouse, and Rat.
• NCBI Home Page NIH's National Library of Medicine NCBI (National Center for Biotechnology Information) link to a tremendous number of resources.

See also a link from the synteny definition:

• Synteny server Server for Synteny Identification and Analysis of Genome Rearrangement—the Identification of synteny and calculating reversal distances.