The macronucleus of the hypotrichous ciliate Oxytricha fallax is transcriptionally active and contains linear achromosomal DNA molecules that function as single-gene units. The terminal organization of macronuclear DNA was analyzed by chemical sequencing and S1 mapping. The terminal sequence of total macronuclear DNA was determined for molecules labeled at the 5' or 3' ends. Results indicate that the 5' sequence C4A4C4A4C4 and the 3' sequence G4T4G4T4G4T4G4T4G4 occur at both ends of all DNA molecules in the macronucleus. The discrepancy in the length of the common terminal sequence between the 5' and 3' ends was clarified by a limited S1 digestion experiment, which indicated the existence of a 16 nucleotide long single-stranded tail at the 3' ends.