Secondary structure models are presented for three pairs of small subunit ribosomal RNA molecules. These are the 16S rRNA from E. coli cytoplasmic and Z. mays chloroplast ribosomes, the 18S rRNA from S. cerevisiae and X. laevis cytoplasmic ribosomes, and the 12S rRNA from human and mouse mitochondrial ribosomes. Using the experimentally-established secondary structure of the E. coli 16S rRNA as a basis, the models were derived both by searching for primary structural homology between the three classes of sequence (12S, 16S, 18S), and also by searching for compensating base changes in putative helical regions of each pair of sequences. The models support the concept that secondary structure of ribosomal RNA has been extensively conserved throughout evolution, differences in length between the three classes of sequence being accommodated in distinct regions of the molecules.