Trisomy of chromosome 20 is associated with the progression of papillary renal cell carcinomas (RCC). To define the gene loci, we have analyzed 40 tumors by applying 18 polymorphic microsatellite markers. An allelic imbalance at all informative loci was seen in 14 cases. Partial duplications of chromosome 20 in 14 tumors delineated four nonsyntenic regions: region A at chromosome 20p12-p13, regions B and C at chromosome 20q11.2, and region D at chromosome 20q13.2. Region B was bracketed by loci D20S206 and D20S478, both mapped to 54 cM and both excluded. The smallest overlapping duplication at region D was scaled down to the region between loci D20S480 and D29S902 marking approximately 100-kb genomic sequences. Allelic duplication in papillary RCC was confirmed by fluorescence in situ hybridisation analysis by using BAC clones 441o14 and 354 n14 positive for the flanking loci at region B. Altogether 70% of papillary RCC showed genetic changes at least at one of the four regions, but coalteration of two or more regions was seen in most cases. (Lab Invest 1999, 79:311-316).