The human 5-HT1A receptor was screened for naturally occurring mutations. The PCR product of the 5-HT1A receptor gene was digested with several restriction enzymes and evaluated by single-strand conformational polymorphism (SSCP) analysis. Comparison of the SSCP electrophoretic pattern with a restriction map of the 5-HT1A receptor allowed localization of the polymorphic sites facilitating their identification by sequence analysis. Two polymorphisms were identified in the human 5-HT1A receptor gene that altered amino acid composition. The polymorphisms encode amino acid substitutions in the 5-HT1A receptor of a glycine to serine at amino acid 22 and an isoleucine to valine at amino acid 28, respectively. Both polymorphisms alter the extracellular amino terminal domain of the 5-HT1A receptor. The polymorphic 5-HT1A alleles have been found in American and Finnish Caucasians and in native American Indians. This is the first report of a polymorphism in the human 5-HT1A receptor gene that alters the structure of the 5-HT1A receptor protein composition.