In this work, all three electrodes in an electrochemical cell were fabricated based on carbon nanotube (CNT) thread. CNT thread partially insulated with a thin polystyrene coating to define the microelectrode area was used as the working electrode; bare CNT thread was used as the auxiliary electrode; and a micro quasi-reference electrode was fabricated by electroplating CNT thread with Ag and then anodizing it in chloride solution to form a layer of AgCl. The Ag|AgCl coated CNT thread electrode provided a stable potential comparable to the conventional liquid-junction type Ag|AgCl reference electrode. The CNT thread auxiliary electrode provided a stable current, which is comparable to a Pt wire auxiliary electrode. This all-CNT thread three electrode cell has been evaluated as a microsensor for the simultaneous determination of trace levels of heavy metal ions by anodic stripping voltammetry (ASV). Hg2+, Cu2+, and Pb2+ were used as a representative system for this study. The calculated detection limits (based on the 3σ method) with a 120 s deposition time are 1.05, 0.53, and 0.57 nM for Hg2+, Cu2+, and Pb2+, respectively. These electrodes significantly reduce the dimensions of the conventional three electrode electrochemical cell to the microscale.