Safe and effective photothermal therapy depends on efficient delivery of heat for killing cells and molecular specificity for targeting cells. To address these requirements, we have designed an aptamer-based nanostructure which combines the high absorption efficiency of Au-Ag nanorods with the target specificity of molecular aptamers, a combination resulting in the development of an efficient and selective therapeutic agent for targeted cancer cell photothermal destruction. Most nanomaterials, such as gold nanoshells or nanorods (NRs), require a relatively high power of laser irradiation (1 x 10 (5)-1 x 10 (10) W/m (2)). In contrast, the high absorption characteristic of our Au-Ag NRs requires only 8.5 x 10 (4) W/m (2) laser exposure to induce 93 (+/-11)% cell death of NR-aptamer-labeled cells. Aptamers, the second component of the nanostructure, are generated from a cell-SELEX (systematic evolution of ligands by exponential enrichment) process and can be easily selected for specific recognition of individual tumor cell types without prior knowledge of the biomarkers for the cell. When tested with both cell suspensions and artificial solid tumor samples, these aptamer conjugates were shown to have excellent hyperthermia efficiency and selectivity. Under a specific laser intensity and duration of laser exposure, about 50 (+/-1)% of target (CEM) cells were severely damaged, while more than 87 (+/-1)% of control (NB-4) cells remained intact in a suspension cell mixture. These results indicate that the Au-Ag nanorod combination offers selective and efficient photothermal killing of targeted tumor cells, thus satisfying the two key challenges noted above. Consequently, for future in vivo application, it is fully anticipated that the tumor tissue will be selectively destroyed at laser energies which will not harm the surrounding normal tissue.