Previous studies from our laboratories have shown that the tissue specificity of alpha 1-antitrypsin (AT) expression differs among closely related mouse species. In laboratory mice (Mus domesticus), AT mRNA is found almost exclusively in the liver. In the wild-derived species Mus caroli, the mRNA is expressed not only in the liver but also in the kidney, where it is regulated by androgens during post-natal development. We presently show that the tissue specificity, the species specificity, and the developmental regulation of AT mRNA levels correlate with the transcription rate of the AT gene, as measured by nuclear run-on assays. During the course of these experiments, we found that some AT-specific probes are complementary to constitutively synthesized RNAs that do not accumulate and that are unrelated to functional AT mRNA expression. These RNAs, which result from both sense and anti-sense transcription, may derive from aberrant initiation events within certain regions of the AT gene.