We have created a program that searches densely genotyped regions for associated non-contiguous haplotypes using a standard family based haplotype association test. This program was designed to expand upon the sliding window methodologies commonly used for haplotype construction by allowing the association of subsets of single nucleotide polymorphisms (SNPs) to drive the construction of the haplotype. This strategy permits HaploBuild to construct more biologically relevant haplotypes that are not constrained by arbitrary length and contiguous orientation.