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This study describes the evaluation of histamine imprinted polypyrrole deposited on boron doped nanocrystalline diamond (NCD). Boron doped oxygen terminated NCD (B : NCD) was used as a conducting substrate for the design of here reported electrochemical sensor. Some peculiarities of B : NCD were evaluated and oxidation kinetics of both NCD and B : NCD was investigated. Both the NCD and B : NCD were modified by molecularly imprinted polypyrrole and not‐imprinted polypyrrole. Histamine was used as a template for molecular imprinting of polypyrrole. Electrochemical impedance spectroscopy was applied for the evaluation of formed MIP and NIP layers.