Rhythmic eclosion of Drosophila adults requires per gene function. We have found that a previously identified 0.9 kb RNA transcribed from DNA adjacent to per becomes abundantly expressed during pupation, just prior to eclosion. The daily synchronized emergence of young adults, coupled with a subsequent rapid decay of the transcript, is responsible for what previously appeared to be cycling of the 0.9 kb RNA in adults. In situ hybridization analyses localize the 0.9 kb transcript to the epidermis of newly eclosed adults. Conceptual translation of genomic DNA and cDNA sequences predicts that the 0.9 kb transcript produces a 261 amino acid protein containing a putative signal sequence for membrane transport at its amino terminus. Pupae that reach the same stage of development at slightly different times of day show a subsequent synchronized rise in 0.9 kb RNA levels, indicating that the expression of this transcript is under circadian clock control.