Molecular imprinting is a technique for preparing polymer scaffolds that function as synthetic receptors1,2,3. Imprinted polymers that can selectively bind organic compounds have proven useful in sensor development2,3,4,5,6,7. Although creating synthetic molecular-imprinting polymers that recognize proteins remains challenging8,9,10,11, nanodevices and nanomaterials show promise in this area12,13,14. Here, we show that arrays of carbon-nanotube tips with an imprinted non-conducting polymer coating can recognize proteins with subpicogram per litre sensitivity using electrochemical impedance spectroscopy. We have developed molecular-imprinting sensors specific for human ferritin and human papillomavirus derived E7 protein. The molecular-imprinting-based nanosensor can also discriminate between Ca2+-induced conformational changes in calmodulin. This ultrasensitive, label-free electrochemical detection of proteins offers an alternative to biosensors based on biomolecule recognition. Carbon nanotube tips containing imprints within a non-conducting polymer coating can detect proteins with high sensitivity, offering a label-free alternative to sensors based on biomolecule recognition.