This article describes the major techniques in molecular genetics, i.e., parametric and nonparametric linkage analyses, association studies and quantitative trait loci approaches. Some major molecular findings in schizophrenia, bipolar affective disorder and Alzheimer disease are presented. Aspects of the complexity of molecular genetic research in psychiatric disorders are discussed, including the relationship between genotype and phenotype, and between etiology and pathophysiology. Molecular findings in two genetic neuropsychiatric disorders, fragile X syndrome and Huntington's disease are described. These findings provoke some critical thoughts regarding future directions in psychiatric molecular research.