An allele (UK: , ; US: ; modern formation from Greek ἄλλος állos, "other") is one of two, or more, forms of a given gene variant. For example, the ABO blood grouping is controlled by the ABO gene, which has six common alleles. Nearly every living human's phenotype for the ABO gene is some combination of just these six alleles. An allele is one of two, or more, versions of the same gene at the same place on a chromosome. It can also refer to different sequence variations for several-hundred base-pair or more region of the genome that codes for a protein. Alleles can come in different extremes of size. At the lowest possible size an allele can be a single nucleotide polymorphism (SNP). At the higher end, it can be up to several thousand base-pairs long. Most alleles result in little or no observable change in the function of the protein the gene codes for.

However, sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. A notable example of this is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of "pure line" traits, that is a single gene with two alleles.

Nearly all multicellular organisms have two sets of chromosomes at some point in their life cycle; that is, they are diploid. In this case, the chromosomes can be paired. Each chromosome in the pair contains the same genes in the same order, and place, along the length of the chromosome. For a given gene, if the two chromosomes contain the same allele, they, and the organism, are homozygous with respect to that gene. If the alleles are different, they, and the organism, are heterozygous with respect to that gene.