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Purpose It is known that despite efforts of improving adequate ablation in head and neck cancer, the local recurrence rate has not decreased sufficiently over the last two decades. This is partly due to the presence of potentially malignant groups of cells in the resection margins (minimal residual disease). Chromosomal instability (CI) detection in these histologically diagnosed tumour-free margins might help predict patients at risk for recurrence. Material and methods We have included 25 patients with oral squamous cell carcinoma (OSCC) treated with surgery alone between 1994 and 2003. All resections were histopathologically radical. Follow-up was documented for at least 5 years. Fluorescence in situ hybridization (FISH) was used to examine all resection margins of all tumours for the presence of CI, which is indicated by the nuclear detection of chromosome imbalances and/or polyploidization for chromosomes 1 and 7. In addition, tissue sections were analysed for p53 expression by immunohistochemistry. Results Of the 25 patients, 11 developed a recurrence. FISH analysis showed that of the 11 recurrences, 8 exhibited CI in at least one resection margin. This relation was significant with a p -value of 0.011. There was a trend for p53 overexpression in the resection margins of tumours with recurrence, however, this trend was not statistically significant ( p = 0.082). Conclusion CI in the resection margins of OSCCs, even though histologically tumour-free, can reliably identify patients at risk for developing a local or locoregional recurrence. A future goal will be to investigate how radiotherapy following surgery influences the prognosis of these patients.