A haplotype is a block of alleles on a chromosome that have a high degree of linkage, often co-segregate in meiosis and are rarely separated by recombination events.

In human genome analysis, haplotypes can be useful in many ways: most notably in homing in on the location of disease-causing alleles. Haplotypes, like all genetic markers, are subject to polymorphisms between individuals. If a particular haplotype is found to be more common among individuals with a disease compared to individuals without the disease, it can strongly indicate that the location of the allele(s) which cause the disease is within that haplotype. The Human HapMap Project was an effort to map all the haplotypes in the human genome precisely for this purpose.

Furthermore, the size of a haplotype can be an indication of the selective forces acting on an allele within that haplotype. Generally alleles that are selectively neutral take many generations to become established in a population. Thus, if a selectively neutral allele is common in a population, it must be an allele that has been present for a long time. The surrounding haplotype is thus likely to be small: many generations of meiosis have passed and the recombination frequency of the haplotype will have been relatively high over that duration of time. Conversely, if an allele is being positively selected then it will generally exist within a large haplotype. This indicates that the allele rose to prominence quickly in the population and few enough generations have passed since its inception that recombination has been scarce.