A highly sensitive electrochemiluminescence (ECL) assay was developed for sequential detection of cardiac troponin I (cTnI) and adenosine triphosphate (ATP) through supersandwich amplification and bifunctional aptamer. The bifunctional aptamer (S1) contained ATP binding aptamer and cTnI binding aptamer. A gold electrode was modified with the specific peptide of cTnI through a self-assembly technique. A sandwichtype conjugate (peptide < cTnI > S1) was formed when the peptide-modified electrode was successively reacted with cTnI and S1. Then, hybridizations between S1 and two ss-DNA auxiliary probes, in which one is complementary with ATP binding aptamer and the other is ATP binding aptamer, led to the formation of long-range ds-DNA on the electrode surface. In the presence of ECL indicator Ru(phen) 3 2 + , a large amount of Ru (phen) 3 2 + was intercalated into ds-DNA grooves, resulting in amplification of the ECL signals. The ECL assay was successfully developed for the detection of cTnI in the range of 8.0 10 À13 to 1.0 10 À11 g/mL based on the increased ECL intensity. After detecting cTnI, ATP was detected in the range of 30 to 500 nM, based on switching structures of aptamers from ds-DNA to ss-DNA/target complex. A low detection limit of 0.3 pg/mL and 10 nM for cTnI and ATP, respectively, was obtained. The employment of a bifunctional aptamer probe and supersandwich signal amplification is promising for the sensitive detection of multiple targets.