Abstract Facile syntheses of [5‐2H]‐, [6‐2H]‐uracil and [5‐2H]‐, [6‐2H]‐cytosine were investigated. The catalytic reaction of uracil or cytosine with 2H2 gas in alkaline media gave rise to [6‐2H]‐compounds almost exclusively. On the other hand,the reaction of 5‐bromouracil or 5‐bromocytosine with 2H2 gas and gave rise to a mixture of [5‐2H]‐, [6‐2H]‐ and [5‐2H,6‐2H]‐compounds depending on the experimental conditions. By controlling the temperature, the pressure of 2H2 gas and the amounts of catalyst, [5‐2H]‐uracil and [5‐2H]‐cytosine were obtained. The isotopic distribution in each product was measured by 1H NMR spectroscopy combined with an HPLC method.