Nanoscale materials are beginning to have an impact in the field of molecular diagnostics. In particular, gold nanoparticles surface-functionalized with DNA have garnered much recent interest. Due to the unusual optical and catalytic properties of gold nanoparticle labels, several distinct advantages for assay readout have been realized. This review focuses on the progress made in our group over the past seven years in the development of particle surface chemistry and ultrasensitive protein and nucleic acid assays based upon DNA-functionalized gold nanoparticles. For DNA targets, experiments demonstrate that assays based upon gold nanoparticle labels have enhanced target specificity and in certain cases the sensitivity of polymerase chain reaction (PCR), without the need for target amplification. For protein targets, similar experiments demonstrate that assays based upon gold nanoparticles are up to one million times more sensitive than conventional protein detection methods. Recent data using human samples demonstrate the utility of such assays.