We describe a sensitive and specific sandwich assay for human alpha-thrombin. The assay takes advantage of sandwich binding of two affinity aptamers for increased specificity, gold nanoparticles for signal amplification, magnetic beads for fast magnetic separation, and inductively coupled plasma mass spectrometry for ultrasensitive detection. Other proteins, such as immunoglobulin G, serum albumin, transferrin, fibrinogen, and lysozyme did not show interference with the assay for human alpha-thrombin. The detection limit of human alpha-thrombin was as low as 0.5 fmol, corresponding to 10 pM thrombin in 50 microL, and the dynamic range covered approximately 3 orders of magnitude.