Owing to their unique chemical and physical properties, colloidal gold nanoparticles have prompted a wide variety of biocompatible nano-agents for cancer imaging, diagnosis and treatment. In this context, biofunctionalized gold nanorods (AuNRs) are promising candidates for light-induced hyperthermia, to cause local and selective damage in malignant tissue. Yet, the efficacy of AuNR-based hyperthermia is highly dependent on several experimental parameters; in particular, the AuNR morphology strongly affects both physical and biological processes. In the present work, we systematically study the influence of different structural parameters like the AuNR aspect ratio, length and molecular weight on in vitro cytotoxicity, cellular uptake and heat generation efficiency. Our results enable us to identify the optimum AuNR morphology to be used for in vivo hyperthermia treatment.