In the hypotrichous ciliate Oxytricha nova all of the macronuclear DNA is in the form of low molecular weight, gene-sized molecules with an average size of 2,200 base pairs. These molecules are produced during macronuclear development by excision from micronuclear chromosomes. All, or nearly all, of the small macronuclear DNA molecules possess an inverted terminal repeat sequence consisting of 5' C4A4 3' repeats. The hypothesis that this terminal sequence serves as a recognition signal for excision of gene-sized molecules from chromosomes has been tested. A sequence containing the C4A4 repeat has been isolated and used to screen clones of micronuclear DNA for the presence of the repeat sequence. The results show that the intact repeated C4A4 sequence is not present at the ends of macronuclear sequences as they exist in the micronuclear chromosomes. Therefore, the entire terminal repeat is not a recognition sequence for gene excision but must be added to the ends of gene-sized molecules during or after the excision process.