The human gene encoding bleomycin hydrolase, a cysteine proteinase involved in chemotherapy resistance, has been cloned, and its overall organization has been established. The gene is composed of 12 coding exons and 11 introns and spans more than 30 kilobases. The number and distribution of exons and introns differ from those reported for other human cysteine proteinases, indicating that these genes are only distantly related. Nucleotide sequence analysis of about 1.2 kilobases of the 5'-flanking region of the human bleomycin hydrolase gene revealed a high GC content, a ratio of CpG/GpC close to unity, and the absence of consensus transcriptional sequences such as TATA box or CCAAT box. All these features are characteristic of housekeeping genes and provide an explanation for the widespread expression of bleomycin hydrolase in human tissues. The 5'-flanking region of the gene also contains a polymorphic CCG trinucleotide repeat that may be a target of genetic instability events and affect its transcriptional activity. Chromosomal localization of the human bleomycin hydrolase gene revealed that it maps to chromosome 17q11.2, very close to the locus of the neurofibromatosis type 1 gene. This location is unique for any cysteine proteinase mapped to date. Finally, Southern blot analysis of DNA from leukocytes and autologous breast tumors has shown that the bleomycin hydrolase gene is not a frequent target of amplification in human breast carcinomas.