About 25% of human neuroblastomas have amplification of the MYCN proto-oncogene, and this feature is associated with advanced stages of disease and rapid tumor progression. Estimates of the size of the amplicon range from 300 to 3,000 kb, with MYCN at or near the center. It has been determined previously that there is considerable conservation of the amplified sequences among different neuroblastomas, and very few rearrangements have been found. We decided to clone the entire amplified domain in YACs to assess the size, structure and organization of the amplified sequences in neuroblastomas and to identify novel or junctional sequences at the ends of an amplicon in double minutes (dmins) or in the germline. A YAC library was constructed from the SMS-KAN cell line, which contains dmins and has about 150 copies of MYCN. About 5,000 clones from this library were screened with MYCN as well as other probes from the amplified domain. To date, 16 YACs have been identified, with a median size of 240 kb (range 50-460 kb). These YAC clones can be arranged in a contiguous, linear map of greater than or equal to 1 megabase. Our data suggest that most neuroblastomas with MYCN amplification also amplify a region that is a megabase or more in size, making this the largest amplified domain cloned to date. The very large size suggests that there are other genes near MYCN whose expression is important in mediating the aggressive phenotype associated with MYCN amplification, or, alternatively, that the nearest origin of replication may be a considerable distance from MYCN.