Pulsed amperometry has been used to detect and discriminate between different base-pair oligonucleotides using flow injection analysis with polypyrrole modified electrodes. Oligonucleotides with 20-repeat units were immobilized as the sole counter anion during polymerisation of pyrrole onto a glassy carbon (GC) electrode. The modified electrode was then used in a flow injection analysis (FIA) set-up to selectively detect complementary oligonucleotides. Results showed that complementary oligo(dG)(20) and non-complementary oligonucleotides can be distinguished by using the oligo(dC)(20) modified electrode.