The first step in the processing of 47S precursor rRNA in mouse cells is reproduced in vitro in an S-100 transcription reaction and consists of an endonucleolytic cleavage at residue +650 of the primary transcript followed by rapid degradation of the fragment upstream from residue +650. An analogous processing occurs in human rRNA. The mouse and human rRNA sequences are approximately equal to 80% conserved for 200 nucleotides on the 3' side of these processing sites, suggesting that this conserved region may be important in specifying the processing. To test this hypothesis, we constructed a systematic series of deletion mutants approaching the mouse rDNA processing region from both the 5' and 3' directions and analyzed the processing of their transcripts in vitro. The 5' boundary of the region required for processing is quite sharp and corresponds to the rRNA cleavage site at the 5' end of the conserved sequence region. The 3' boundary is more complex: The 3' deletions extending to between 250 and 130 nucleotides beyond the processing site cause about a 50% decrease in the amount of the processed RNA. A 3' deletion that extends to 109 nucleotides beyond the processing site greatly reduces the processing efficiency. Deletions to or beyond 91 nucleotides on the 3' side of the processing site virtually eliminate processing. Under altered ionic conditions, transcripts of 3' deletions extending to only 41 nucleotides beyond the processing site can still direct a low level of accurate processing. These results demonstrate that the mouse/human conserved sequence just on the 3' side of the primary rRNA processing site consists of several domains that direct and/or augment both the initial endonucleolytic cleavage and the closely coupled selective degradation of the upstream fragment that together constitute the primary rRNA processing event.