We evaluated the involvement of tyrosine hydroxylase (TH) mutations in susceptibility to manic-depressive disease (MDD) and alcoholism (ALC) with a cladistics-based association analysis. Eighty-one probands with MDD, 113 probands with alcoholism, and 80 normal controls were tested for differences in frequency of nine haplotypes at the TH locus. The haplotypes were comprised of four restriction fragment length polymorphisms spanning the TH gene. A cladogram constructed from the haplotypes provided the evolutionary context for a nested statistical analysis. Statistically significant evidence was found for association of a subgroup of the sample for each of the disorders with different branches of the gene tree, but the findings were sensitive to minor changes in estimated haplotype frequencies.