In boron neutron capture therapy, the absorbed dose from the ¹⁰B(n,α)⁷Li reaction depends on the ¹⁰B concentration and ¹⁰B distribution in the irradiated volume. Thus compounds used in BNCT should have tumor-specific uptake and low accumulation in normal tissues. This study compares in a mouse model the ¹⁰B uptake in different organs as delivered by l-para-boronophenylalanine (BPA, 700 mg/kg body weight, i.p.) and/or sodium mercaptoundecahydro-closo-dodecaborate (BSH, 200 mg/kg body weight, i.p). After BSH injection, the ¹⁰B concentration was high in kidneys (20 ± 12 µg/g) and liver (20 ± 12 µg/g) but was low in brain (1.0 ± 0.8 µg/g) and muscle (1.9 ± 1.2 µg/g). After BPA injection, the ¹⁰B concentration was high in kidneys (38 ± 25 µg/g) and spleen (17 ± 8 µg/g) but low in brain (5 ± 3 µg/g). After combined BPA and BSH injection, the effect on the absolute ¹⁰B concentration was additive in all organs. The ratio of the ¹⁰B concentrations in tissues and blood differed significantly for the two compounds depending on the compound combination, which implies a different uptake profile for normal organs.