Molecular imprinting is a technique for preparing polymer scaffolds that function as synthetic receptors. Imprinted polymers that can selectively bind organic compounds have proven useful in sensor development. Although creating synthetic molecular-imprinting polymers that recognize proteins remains challenging, nanodevices and nanomaterials show promise in this area. 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 Ca(2+)-induced conformational changes in calmodulin. This ultrasensitive, label-free electrochemical detection of proteins offers an alternative to biosensors based on biomolecule recognition.