Human ribosomal protein (rp) S26e is known to bind to the first intron of its pre-mRNA and, thus, inhibit mRNA splicing. In this work, the hydroxyl radical footprinting was applied for the detailed mapping of the rpS26e binding site on the RNA transcript that corresponds to the rpS26e pre-mRNA fragment containing the first intron flanked by the sequences of the first exon and a part of the second exon. Nucleotides protected from the hydroxyl radical attack in the presence of rpS26e were identified. Most of them were found in the region of the 3' splice site of the first intron within the purine-rich sequence, which forms a loop between two helices in the predicted secondary structure of the rpS26e pre-mRNA fragment, and the remaining nucleotides are located near the 5' splice site. A comparison of the arrangements of the rpS26e binding sites on the pre-mRNA and 18S rRNA secondary structures revealed similar elements in the organization of these sites. It was found that both sites contained a uniform structural motif, namely an extended purine-rich loop between two helices, which could be recognized by rpS26e upon binding to these RNAs. The results shed light on the structural aspects of the RNA-protein interactions, which underlie the autoregulation of the human RPS26e gene expression at the splicing step.