Iron oxide based nanoparticles are finding their way as leading actors in nanotechnology applications to medicine. Magnetite nanoparticles are currently being used in clinics for the detection of hepatic tumors based on their unspecific accumulation in liver. More and more works are being published on potential applications of magnetic nanoparticles in diagnostics and therapy. But the interaction between magnetic nanoparticles and human cells at the subcellular level is only now beginning to be studied and more basic research is needed in this field. This work studies the interaction between carbohydrate functionalized gold-coated magnetite nanoparticles and C33 tumoural human cells as the first step towards the in vivo application of these nanoparticles. The uptake of this magnetic material follows a similar trend to that described for other nanoparticles. The intracellular fate of these nanoparticles once internalized has been unveiled, and an automatic methodology for the analysis of co-localization data has also been tested and compared to a more classic approach. These results can help in the optimization of the design of magnetic nanoparticles depending on their final application.