A series of bis-benzimidazole compounds with a head-to-head orientation have been designed as sequence-specific DNA binders; crystallographic analysis of oligonucleotide complexes has been combined with DNase I footprinting to confirm that the predicted optimal site for the core bis-benzimidazole motif is the four-base-pair sequence 5′-AATT; this sequence specificity results in inhibition of transcription at A/T sites and may be responsible for the cytotoxic and antitumour effects shown by these head-to-head bis-benzimidazoles.