Alleles are corresponding pairs of genes located at specific positions in the chromosomes. Together, alleles determine the genotype of their host organism. For example, the alleles for eye color are found on chromosomes 15 and 19, and depending on which alleles someone has, he or she may have blue, brown, green, gray, or hazel eyes, and sometimes a mixture of these traits is present. Alleles which determine some aspect of the phenotype, the physical appearance of an organism, are said to be “coding alleles,” while “non-coding alleles” or “junk DNA” are alleles which do not appear to have an impact on phenotype.

There are numerous combinations of alleles, ranging from simple pairs to complex relationships between multiple alleles which determine someone's appearance. When both of the alleles in a pair are the same, the alleles are is said to be “homozygous,” while if the alleles are different, the situation is described as “heterozygous.” In the case of homozygous alleles, the expression of phenotype is usually very straightforward. In heterozygous instances, however, the phenotype of the organism is determined by which allele is dominant, meaning that one allele overrides the other.

In the case of eye color, if someone inherits a blue allele and a brown allele, his or her eyes will be brown, because brown is a dominant genetic trait, requiring only one allele for expression. However, if that person had a child with someone who also carried a blue allele and both parents passed the blue trait down, the child would have blue eyes. This explains why blue-eyed children sometimes randomly pop up in a brown-eyed family: because someone in the family's genetic history had blue eyes.

Researchers are constantly identifying new alleles, and developing specific tests to look for certain alleles, especially those linked with genetic conditions or genetic predispositions to disease. In genetic testing for conditions like Huntington's Disease, a medical lab can search for the specific spot on chromosome four where the Huntington's allele resides. Unfortunately, Huntington's is a dominant trait, so it only takes one allele to develop the condition.

Alleles are also utilized in DNA tests used to establish a connection between a known DNA sample and an unknown sample. Crime labs, for example, test DNA evidence from crime scenes against known DNA databases and potential suspects, and DNA tests are also used to test the parentage of children. Such testing is often extremely accurate, as long as the samples are handled properly and they are of good quality.