The Hardy-Weinberg equilibrium can be generalized to haplotypes involving two (or more) loci. When there is no linkage between the alleles, say and with dominant frequencies and , respectively, the genotypes and phenotypes are simply products of two independent H–W distributions. Linkage disequilibrium can occur if the allele frequencies influence one another. This can be quantified by a parameter , such that the composite haplotype frequencies are given by , , , and . If no linkage occurs, . In this Demonstration, the 16 possibilities for offspring genotypes are plotted on a two-dimensional bar chart. Because the maximum possible value for cannot exceed any allele frequency, the slider will sometimes move as you drag an allele frequency slider.

For purposes of illustration, the two traits are chosen to be hair color (brown or blond) and eye color (brown or blue), with brown dominant in both cases. This is actually a gross oversimplification: in real life, the genetics of hair and eye color are much more complex. (For example, coauthor S. M. Blinder, offspring of parents with blue and brown eyes, finds himself with green eyes!)