Summry—Extensive developmentally programmed DNA rearrangements, including thousands of internal deletions, occur in the differentiating somatic macronucleus inTetrahymena thermophila. Some deletion systems involve the use of multiple alternative deletion sites. We report here the cloning and the sequences of three new alternative deletion systems (RR, RP and B) obtained using genomic subtraction. The RP and RR deletion systems are 2 kb apart on chromosome IR, and both involve the removal of5 kb. All three deleted regions are very AT rich (∼ 80%) and do not appear to encode any protein. Sequences of the regions flanking the deletion junctions of all three systems revealed no sequence similarity among them nor with any previously reported deletion systems, suggesting that differentcis‐acting elements are involved for rearrangement. Unlike other deletion systems in ciliates, the B deletion system lacks short terminal direct repeats. Our results suggest an average of at least one alternative deletion system per 134 kb of micronuclear DNA and lead to an estimate that at least 25% of all deletion systems inTetrahymenautilize alternative ends. The genomic subtraction method employed in this study could prove useful for the isolation of alternatively deleted DNA in special‐purpose cases inTetrahymenaand other ciliates. The hybridization parameters for genomic subtraction worked out here for highly AT‐rich DNA may have wider u