Magnetic hyperthermia has a significant potential to be a new breakthrough for cancer treatment. The simple concept of nanoparticle-induced heating by the application of an alternating magnetic field has attracted much attention, as it allows the local heating of cancer cells, which are considered more susceptible to hyperthermia than healthy cells, while avoiding the side effects of traditional hyperthermia. Despite the potential of this therapeutic approach, the idea that local heating effects due to the application of alternating magnetic fields on magnetic nanoparticle-loaded cancer cells can be used as a treatment is controversial. Several studies indicate that the heating capacity of magnetic nanoparticles is largely reduced in the cellular environment due to increased viscosity, aggregation and dipolar interactions. However, an increasing number of studies, both in vitro and in vivo, show evidence of successful magnetic hyperthermia treatment on several different types of cancer cells. This apparent contradiction might be due to the use of different experimental conditions. Here we analyze the effects of several parameters on the cytotoxic efficiency of magnetic nanoparticles as heat inductors under an alternating magnetic field. Our results indicate that cell-nanoparticle interaction reduces the cytotoxic effects of magnetic hyperthermia, independently of nanoparticle coating and core size, the cell line used and the subcellular localization of nanoparticles. However, there seems to occur a synergistic effect between the application of an external source of heat and the presence of magnetic nanoparticles, leading to higher toxicities than those induced by heat alone, or the accumulation of nanoparticles within cells.