Human ribosomal protein (rp) S16 is a homologue of prokaryotic rpS9 that contacts the 16S rRNA region formed by helices H29, H30. H38-40, H41, H43 according to X-ray crystallography data on the 30S ribosomal subunit. In the present work, we report studying interaction of human recombinant rpS16 with a RNA transcript corresponding to the region 1203-1236/1521-1698 (helices H28-30 and H41-43) of human 18S rRNA, which is homologous to the 16S rRNA region known to bind rpS9. RpS16 was shown to specifically bind to the transcript forming a stable complex with the apparent dissociation constant of (1.3 +/- 0.1) x 10(-8) M at 20 degrees C. Nucleotide residues of the transcript that change their accessibility to RNases and modifying chemical probes upon the rpS16 binding were determined by enzymatic and chemical footprinting. It was shown that rpS16 causes significant enhancement of reactivities of nucleotides C1544 (internal loop of helix H41), C1618-U1622 and C1629-A1634 (helix H42), C1521-C1523, U1530, C1532 (helix H30) and C1645, C1646, G1648 (helix H43) and protection of nucleotides C1670-A1675 (helix H43). In the bacterial 30S ribosomal subunit many of those nucleotides of 16S rRNA that correspond to 18S rRNA nucleotides mentioned above contact rpS9 amino acid residues.