We have cloned the human perforin (P1) gene and sequenced 6.2-kb genomic DNA, containing 1.4-kb 5'-flanking region, the 5' untranslated region, the complete coding region and the beginning of the 3' untranslated region. The P1 gene including at least 95-bp 3' untranslated region is organized in only three exons: the first exon (97 bp) contains all but four nucleotides of the 5' untranslated region and was determined by primer extension and S1 nuclease mapping. This exon is separated by 1.7 kb from the second exon containing the remaining (4 bp) 5' untranslated region, the leader peptide and the N-terminal region of P1 up to--but not including--the C9 homologous region. The third exon is separated by a 1.2-kb intron and contains the remainder of the molecule, including at least 90 bp of the 3' untranslated region. This simple gene organization differs from that of the more complicated C9 gene. Because of the unusual intron in the 5' untranslated sequence the transcription initiation (cap) site is located almost 1.8 kb upstream of the ATG start signal. The more immediate 5' flanking sequence contains a CCAAT and GC box but lacks other known promoter elements. Instead, we find three different sequence repeats. One of them, a hexanucleotide sequence with the consensus GCCCTG of unknown significance occurs 19 times within a stretch of 240 bp. Further upstream we localized sequences homologous to the following enhancer and promoter elements: c-fos proto-oncogene, IFN-gamma and phorbol ester response elements, five cAMP response elements, and three motifs corresponding to general inducer elements. In addition, a sequence conserved in the 5'-flanking region of several T cell genes was identified. The 5' flanking regions of P1. CCP1 (granzyme B) and CCP2 (granzyme C) (kindly provided by Dr. Bleackley) contain as only significant homology cAMP response elements. These findings are consistent with a tight control and regulation of P1, which appears to be distinct from that of granzymes.