Boron neutron capture therapy (BNCT) provides highly targeted delivery of radiation through the limited spatial distribution of its effects. This translational research/phase I clinical trial investigates whether BNCT might be developed as a treatment option for squamous cell carcinoma of head and neck (SCCHN) relying upon preferential uptake of the two compounds, sodium mercaptoundecahydro-closo-dodecaborate (BSH) or L-para-boronophenylalanine (BPA) in the tumour. Before planned tumour resection, three patients received BSH and three patients received BPA. The 10B-concentration in tissues and blood was measured with prompt gamma ray spectroscopy. Adverse effects from compounds did not occur. After BPA infusion the 10B-concentration ratio of tumour/blood was 4.0 ± 1.7. 10B-concentration ratios of tumour/normal tissue were 1.3 ± 0.5 for skin, 2.1 ± 1.2 for muscle and 1.4 ± 0.01 for mucosa. After BSH infusion the 10B-concentration ratio of tumour/blood was 1.2 ± 0.4. 10B-concentration ratios of tumour/normal tissue were 3.6 ± 0.6 for muscle, 2.5 ± 1.0 for lymph nodes, 1.4 ± 0.5 for skin and 1.0 ± 0.3 for mucosa. BPA and BSH deliver 10B to SCCHN to an extent that might allow effective BNCT treatment. Mucosa and skin are the most relevant organs at risk.