We describe a shape-controlled synthesis of polyelectrolytefunctionalized flowerlike and polyhedral Au nanoparticles and the development of a nanoarchitectured platform for the selective and highly sensitive detection of protamine and heparin by voltammetric, impedimetric, and microgravimetric techniques. The functionalized Au nanoparticles were chemically synthesized in aqueous solution at room temperature in the presence of the polyelectrolyte (either protamine or heparin). The charge on the polyelectrolyte controlled the shape and surface morphology of the nanoparticles. The negatively charged heparin-functionalized Au nanoparticles have multiple branched flowerlike shapes with an average size of 50 nm, whereas the cationic protamine-functionalized nanoparticles are of polyhedral shape with an average size of 25 nm. Both flowerlike and polyhedral nanoparticles have (111), (200), (220), and (311) planes of a face-centered cubic lattice of Au. Voltammetric, impedimetric, and microgravimetric sensing platforms based on functionalized Au nanoparticles have been developed for the sensing of heparin and protamine. The sensing platforms are developed by self-assembling the functionalized nanoparticles on a thiol-functionalized three-dimensional silicate network. The microgravimetric sensing platform shows very high sensitivity and it can detect heparin and protamine at concentrations as low as 0.05 μgmL-1. The selectivity of the sensing platform towards heparin was examined with potential interferents such as hyaluronic acid (HA) and chondroitin-4-sulfate (CS). Both HA and CS did not interfere with the measurement of heparin. The practical application of the sensing platform was demonstrated by measuring the concentration of heparin and protamine in human serum samples. The sensing platform could successfully quantify the concentration of heparin and protamine in the real serum samples with excellent recovery. The sensing platform was robust and could be used for repeated measurement without compromising the sensitivity.