Gold nanorods (GNR) use has been proposed in medical applications because of their intrinsic photothermal properties. However, the presence of CTAB molecules adsorbed onto the surface of GNRs results in a highly cytotoxic GNR system. In this work we replace the CTAB molecules with a thiolated chitosan. Once chitosan coated GNRs (Chi-SH-GNR) were attained, a film of alginate (Alg-Chi-SH-GNR) or polyvinyl alcohol (PVA-Chi-SH-GNR) was deposited onto the surface of Chi-GNR by a layer-by-layer process. The photothermal conversion efficiency for the GNR systems was determined irradiating the GNRs suspended in aqua media with a CW 808nm diode laser (CNI, China). The cytotoxicity effect and the photothermal cellular damage of GNR systems were evaluated on a breast cancer cell line. Results show that polymer coats did not affect the transduction photothermal efficiency. Values around 50% were obtained for the different coated gold nanorods. The cytotoxicity of coated gold nanorods diminished significantly compared with those GNR stabilized with CTAB. The laser irradiation of cells treated with gold nanorods showed a decrease in their viability compared with the cells treated but no irradiated.