Nanocrystalline apatites with different Ca/P ratios were synthesized using eggshell as a calcium source by microwave processing. The apatites were found to have a minor amount of Mg, Sr, Si and Na ions inherited from the eggshells. The presence of several foreign ions results in a perturbed lattice structure indicated by an increase in lattice constants and shift in vibrational frequencies of the functional groups. The apatites were heat treated to investigate the influence of foreign ions on thermal stability. The minor amounts of ions do not affect the thermal stability. The differences in thermal behaviour of these apatites were due to the presence of HPO2- 4 ions only and not due to other ions because of their low content. © 2009 IOP Publishing Ltd.