The human NACP/alpha-synuclein gene has been cloned. This gene consists of 6 exons ranging in size from 42 to 1110 bp. The translation start codon ATG is encoded by exon 2 and the stop codon TAA is encoded by exon 6. The non-Abeta component of Alzheimer's disease amyloid (NAC) is encoded by exon 4. The two previously reported minor isoforms of NACP/alpha-synuclein, NACP112 [29] and NACP126 [6], are alternatively spliced products, in which exon 5 and exon 3 are spliced out, respectively. Exon 1 was found to have different splicing sites, producing different 5'-untranslated sequences in the cDNAs. A previously reported dinucleotide repeat polymorphic marker has been mapped to 8kb upstream of the transcription start site. A highly TC-rich sequence in intron 4 was found to be polymorphic by length and four alleles, A0, A1, A2 and B have been identified in the Caucasian population. Genotyping this polymorphism among pure Alzheimer's, Lewy body variant and Parkinson's subjects and aged normal control subjects did not reveal any significant differences.