Objective: The response of tumours to fractionated radiotherapy is determined by many factors including repopulation, reoxygenation, the number of clonogenic cells, and their intrinsic radiosensitivity. However, after single radiation doses given under conditions of clamp hypoxia, the dose to control a tumour locally is dependent only on the number of clonogenic cells and their cellular radiosensitivity. Therefore, these parameters were investigated using local control after single doses given under hypoxia, to predict the outcome of fractionated irradiation. Materials and methods: Ten hSCC cell lines (FaDu, UT-SCC-15, UT-SCC-14, XF354, UT-SCC-5, UT-SCC-45, SAS, CAL-33, UT-SCC-8, and HSC-4) were transplanted subcutaneously into the right hind-leg of NMRI nude mice. At 7 mm in diameter, tumours were irradiated either with graded single doses under clamp blood flow conditions (n = 873) or with 30 graded fractions within 6 weeks (n = 905) under ambient conditions. Local tumour control was determined 120 days after irradiation. Radiation response was quantified in terms of TCD₅₀, i.e. the dose required to control 50% of tumours locally. Results: Ten tumour lines investigated showed a pronounced heterogeneity in both TCD_50(30fx/6w) after fractionated irradiation and TCD_50(SDclamp) after single dose irradiation. TCD_50(30fx/6w) varied between 45 Gy for UT-SCC-45 and 127 Gy for SAS; TCD_50(SDclamp) varied between 42 Gy for UT-SCC-14 and 66 Gy for CAL-33. Two tumours were excluded from further analysis due to immunogenicity or non-defined TCD₅₀. Linear regression analysis revealed a significant positive correlation between TCD_50(SDclamp) and TCD_50(30fx/6w) (R² = 0.82, p = 0.002). Conclusions: Significant association between TCD_50(SDclamp) and TCD_50(30fx/6w) suggests that the pre-treatment number of clonogenic tumour cells and their cellular radiosensitivity have a major impact on local control after fractionated radiotherapy.