Prostaglandin (PG) synthesis during inflammation occurs mainly via the transcriptionally regulated cyclooxygenase, COX-2. In pulmonary type II A549 cells, Northern analysis identified multiple IL-1 beta-inducible COX-2 mRNA transcripts. Amplification of 3'-cDNA ends by anchored PCR revealed products corresponding to the predominant 4.5 and 2.7 kb transcripts. Sequence analysis of amplification products indicated that these transcripts arose by alternate consensus and non-consensus polyadenylation site usage. The predominant 4.5 kb transcript showed a half-life in excess of two hours that was further stabilized by IL-1 beta. In addition, the COX-2 3'-untranslated region (UTR), which contains 22 copies of the putative RNA instability motif, AUUUA, when cloned downstream of a constitutively expressed luciferase gene, was found to confer partial IL-1 beta responsiveness in LA-4 cells. Finally, in vivo in LPS-treated rats, differential expression of similar COX-2 mRNA isoforms was also observed. Taken together these data suggest a functional role for post-transcriptional mechanisms, including alternate polyadenylation, in the control of COX-2.