HepG2 cell death with magnetic hyperthermia (MHT) using hydroxyapatite nanoparticles (mHAPs) and alternating magnetic fields (AMF) was investigated in vitro. The mHAPs were synthesized as thermo-seeds by co-precipitation with the addition of Fe2+. The grain size of the HAPs and iron oxide magnetic were 39.1 and 19.5 nm and were calculated by the Scherrer formula. The HepG2 cells were cultured with mHAPs and exposed to an AMF for 30 min yielding maximum temperatures of 43 ± 0.5 °C. After heating, the cell viability was reduced by 50% relative to controls, lactate dehydrogenase (LDH) concentrations measured in media were three-fold greater than those measured in all control groups. Readouts of toxicity by live/dead staining were consistent with cell viability and LDH assay results. Measured reactive oxygen species (ROS) in cells exposed to MHT were two-fold greater than in control groups. Results of cDNA microarray and Western blotting revealed tantalizing evidence of ATM and GADD45 downregulation with possible MKK3/MKK6 and ATF-2 of p38 MAPK inhibition upon exposure to mHAPs and AMF combinations. These results suggest that the combination of mHAPs and AMF can increase intracellular concentrations of ROS to cause DNA damage, which leads to cell death that complement heat stress related biological effects.