A chemical procedure to replace the cetyltrimethylammonium bromide (CTAB) cap on gold nanorods (GNRs) fabricated through seed-mediated growth with organothiol compounds [3-animo-5-mercapto- 1,2,4-triazole (AMTAZ) and 11-mercaptoundecaonic acid (MUDA)] was developed to reduce the cytotoxity of GNRs and facilitate further biofunctionalization. Compared to phosphatidylcholine (PC) modification, our procedure yields stable GNRs that are biocompatible and suitable for whole-cell studies. The PC-, AMTAZ-, and MUDA-activated GNRs all showed low cytotoxicity. By choosing different organothiols, net positive or negative charges could be created on the nanorod surface, for different applications. Gold nanorod molecular probes (GNrMPs) were fabricated by subsequent attachment of antibodies to the activated GNRs and were used to visualize and detect cell surface biomarkers in normal and transformed human breast epithelial cells, demonstrating the potential of developing novel biosensors using gold nanorods. The sensitivity of GNrMPs made from organothiol-activated GNRs is considerably higher than that of CTAB/PC-activated GNRs, demonstrating that the protocol reported here is favored in developing molecular probes using GNRs.