The fluorescence in situ hybridisation (FISH) technique is now well established for retrospective dosimetry in cases of external radiation exposure that occurred many years ago. However, the question remains as to whether FISH provides valid estimates of cumulative red bone marrow radiation doses in cases of incorporation of radionuclides or combined external and internal exposures. This question has arisen in connection with the interpretation of results of dose assessments for epidemiological studies of plutonium workers at the Russian Mayak plant and of members of the public exposed to strontium radioisotopes and external radiation as a result of discharges from Mayak to the Techa River. Exposures to penetrating external radiation result in fairly uniform irradiation of body tissues, and hence similar doses to all tissues, for which FISH dosimetry can provide a reliable measure of this whole body dose. However, intakes of radionuclides into the body by inhalation or ingestion may result in retention in specific organs and tissues, so that the distribution of dose is highly heterogeneous. For radionuclides emitting short-range radiations (e.g. alpha particles), this heterogeneity can apply to dose delivery within tissues and between cells within tissues. In this paper, an attempt is made to address the question of what FISH measures in such circumstances by considering evidence regarding the origin and lifetime dynamics of lymphocyte subsets in the human body in relation to the localised delivery of dose from the internal emitters 90Sr and 239Pu, which are of particular interest for the Southern Urals Mayak and Techa River populations, and for which most evidence is available in these populations. It is concluded that the FISH translocation assay can be usefully applied for detecting internal and combined external gamma and internal doses from internally deposited 90Sr, albeit with fairly large uncertainties. The same may be true of 239Pu, as well as other radionuclides, although much work remains to be done to establish dose-response relationships.