Childhood-onset mood disorder (COMD) is a condition with pronounced morbidity. Brain-derived neurotrophic factor (BDNF) has antidepressant-like effects at cellular and molecular levels in animals; variants of the BDNF gene have been associated with bipolar disorder. Two BDNF polymorphisms, a dinucleotide repeat, (GT)n, and a single nucleotide polymorphism (SNP), Val66 Met, were genotyped in 99 adults with COMD and matched controls. The BDNF (GT)n marker was associated with COMD (168 bp OR = 3.94, CI = 1.72 to 9.04). Alleles of Va166Met were not associated with COMD. The haplotype val/short contributes to risk.Studies in several species have implicated BDNF and catechol-O-methyltransferase (COMT) in memory. In 63 young adults with a history of COMD, we genotyped three BDNF polymorphisms and the COMT Val108/158 Met SNP. Multivariate analysis of variance (MANOVA) was employed to test hypotheses of association. We found no evidence of association between the two loci and declarative memory phenotypes.