Each telomere in a single strain (S288C) of Saccharomyces cerevisiae was marked with a URA3 containing integrating vector having telomeric TG1-3 sequences. Efficiency of integrative transformation was enhanced by creating single random double-strand breaks in the integrating vector using DNAseI in the presence of Mn2+ ions. A total of 327 transformants were screened by CHEF gels of intact chromosomal DNA. Transformants with homology to the vector at particular chromosomal bands were then screened by Southern analysis with several restriction enzymes to confirm telomeric locations. CHEF gels of NotI and/or SfiI digests were also analyzed to determine left or right arm locations. In some cases allelism of marked telomeres was determined genetically. Transformation was performed by lithium acetate and electroporation with varying results. Electroporation resulted in 50% (75/150) of the integrants at the internal URA3 location rather than telomeres. There were also two rearrangements involving URA3 and the telomere of another chromosome. Lithium acetate transformation resulted in fewer integrants at the internal URA3 location (5/84) and no rearrangements. All telomeres were marked with approximately the same efficiency ranging from 0 to 11 hits in the first 240 transformants. These marked telomeres can be used to complete the physical maps of chromosomes in which the telomere regions are absent. The marked telomeres can be cloned with the appropriate restriction enzymes, thus completing the cloning of individual chromosomes for sequencing projects. The analysis of these clones will lead to a better understanding of telomere region biology. The methodology can also be applied to telomeres of other organisms once they are cloned as telomeric YACs.