In this paper we present fluorine analysis by transmission electron microscopy (TEM-EDX) and measurement of concentration profiles by nuclear reaction analysis with a proton beam (PIGE and microPIGE) on various archaeological bone and dentine material. Fluorine is present as trace element in modern bone and dentine (100–1000 ppm) whose mineral phase consists of a poorly crystalline hydroxylapatite (Ca10(PO4)6 − x(CO3)x(OH)2+x). During the burial time, archaeological bone and dentine accumulate F in the apatite structure. TEM-EDX can evidence fluorine accumulation on a very localised, nanometric scale if its concentration exceeds 1 wt.%. On the contrary, PIGE and microPIGE permit detection of fluorine with a high sensitivity (limit of detection 30 ppm) on a microscopic or macroscopic level. Its spatial resolution can be of 10 µm, but is, however, insufficient to resolve the distribution of fluorine within the bone and dentine apatite nanocrystals. We show the complementarity of the information delivered by each technique on examples of ancient bone and dentine remains from different archaeological and geological sites, dating from the Neolithic Age to the Miocene.