Intracellular calcium (Ca2+) is a key signaling element that is involved in a great variety of fundamental biological processes. Thus, Ca2+ deregulation would be involved in the cancer cell progression and damage of mitochondrial membrane and DNA, which lead to apoptosis and necrosis. In this study, we have prepared amorphous calcium phosphate nanoparticles (ACP NPs) for studied their incorporation by endocytosis or electroporation to epithelial, endothelial and fibroblast cells (MCF-7, HUVEC and COS-1 cells, respectively). Our results showed that internalized ACP NPs have cytotoxic effects as a consequence of the increase of the intracellular calcium content. The endocytosis pathways showed a greater cytotoxic effect since calcium ions could easily be released from the nanoparticles and be accumulated in the lysosomes and mitochondria. In addition, the cytotoxic effect could be reversed when calcium ion was chelated with ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid (EGTA). Modification of ACP NPs by coating with different compounds based on phosphates was also evaluated. The results indicated a reduction of the cytotoxic effect, in the order polyphosphate < phosphonic acid < orthophosphate. A differential cytotoxic effect of ACP-NPs was observed in function of the cell type; the cytotoxic effect can be ordered as i.e., HUVEC > COS-1 > MCF-7. The greater cytotoxic effect caused by the increase of intracellular calcium that is observed in normal cells and the greater resistance of cancer cells suggests new perspectives for cancer research.