To examine the expression of genes encoding rare transcripts in the rat brain, we have characterized genomic DNA clones corresponding to this class. In brain cells, as in all cell types, rare transcripts constitute the majority of different sequences transcribed. Moreover, when compared with other tissues or cultured cells, brain tissue may be expected to have an even larger set of rare transcripts, some of which could be restricted to subpopulations of neural cells. We have identified seven clones whose transcripts are nonabundant, averaging less than three copies per cell. Clone rgl3 (rat genomic 13) RNA was detected only in the brain, whereas RNA of a second clone, rg4O, was also detected in the brain and in a melanoma. Transcripts of rgl3 were found in cerebellum, cerebral cortex, and regions underlying the cortex, whereas rg4O transcripts were not detected in the cerebellum. Transcripts of both rgl3 and rg4O were found in pelleted polysomal RNA. RNA of another clone, rg34, was found in the brain, liver, and kidney but was found in pelleted polysomal RNA only in the brain, suggesting that its expression may be post-transcriptionally controlled. The remaining four clones represent rare transcripts that are common to the brain, liver, and kidney; rgl8 RNA is restricted to the nucleus, whereas rg3, rg26, and rg36 transcripts are found in the cytoplasm of all three tissues. Transcripts of the brain-specific clone, rgl3, and the commonly expressed clone, rg3, are nonpolyadenylated, presumably belonging to the high-complexity, nonpolyadenylated class of transcripts in the mammalian brain.The mammalian brain, the most complex organ in terms of function and structure, is also the most complex in terms of the diversity of its transcripts. The diversity or complexity of an RNA population can be measured by hybridizing RNA in excess to trace amounts of radioactive, nonrepetitive (unique-sequence) DNA, such that the amount of DNA driven into hybrids at saturation gives a direct measure of the percentage of nonrepetitive DNA transcribed. Complexity measurements have consistently shown that brain RNA in rodents displays a greater complexity than RNA from other tissues (mouse tissue [2,6,15,16,19,26,49]; rat tissue [8,9,13,14,17,25,28,43,47,51]). For example, Chikaraishi et al. (9) have found the nuclear RNA complexity of rat brain (31.2% of unique-sequence DNA coding capacity, assuming asymmetric transcription) to be higher than that of liver (21.8%) or kidney (10.6%).A higher proportion of nuclear RNA complexity (nearly two-thirds) is conserved as cytoplasmic or polysomal RNA in the brain than in the liver or kidney (3, 8)