BACKGROUND: Secondary neutrons generated during proton radiotherapy and high-energy photon radiotherapy have been highlighted as a risk factor for secondary malignancies. Proton therapy reduces dose outside the target volume and extends survival rates, therefore clarifying the effects of unwanted neutron exposure is doubly important. Low-energy thermal neutrons comprise a notable portion of these secondary neutron radiation fields. Previously, we carried out theoretical microdosimetry evaluations which indicated that the mean quality factor for thermal neutrons were about 10 times the radiation weighting factor of 2.5 recommended by the International Commission on Radiological Protection (ICRP). Here, we describe low-dose experimental studies that examine the relative biological effectiveness of thermal neutrons, as compared to reference gamma radiations. METHODS: Whole blood was irradiated with a thermal neutron beam, with an average energy of 64 meV, from the National Research Universal reactor located at Canadian Nuclear Laboratories. Absorbed doses ranged from 6 mGy to 85 mGy. DNA damage was evaluated in lymphocytes using the dicentric chromosome assay (DCA) and the cytokinesis-block micronucleus assay (CBMN), and apoptosis was evaluated by the Annexin V assay. RESULTS: A linear dose response was found for all endpoints. The DCA and the CBMN assay generated similar maximum relative biological effectiveness (RBEM) values of 11.3 ± 1.6 and 9.1 ± 1.6, respectively. Surprisingly, analysis of apoptotic induction found a lower RBEM of 3.6 ± 1.3. The theoretical and measured DNA damage values are much higher than the RBEM of 1 and 1.1 assigned to photons and protons, respectively. CONCLUSIONS: This work furthers the understanding of the biological consequences of low-energy thermal neutrons and confirms that extraneous neutrons are of potential concern to the long-term survival of patients that undergo proton radiotherapy.