The structure of human 40S ribosomal subunits has been probed by a cross-linking strategy based on the use of oligonucleotide derivatives that modify proteins in the vicinity of specific 18S rRNA sequences. The oligonucleotide derivatives carried a p-azidoperfluorobenzamide group at the 5′ ends and were complementary to 18S rRNA sequences 609–618 and 1047–1061, homologous to the highly conserved regions designated as the “530 stem-loop” and “790 stem-loop”, respectively, in Escherichia coli 16S rRNA. Ribosomal proteins surrounding these sequences were the main targets of the cross-linking. Proteins S3 and S5 were cross-linked to the derivative complementary to the sequence 609–618, and proteins S2 and S3 were modified by the derivative complementary to the sequence 1047–1061. Cross-linking was not affected by binding of 40S subunits to either poly(U) or poly(U) and Phe-tRNAPhe.