Open AccessStudies employing a single protein nanopore as a molecular recognition element in the development of analytical devices - biosensors, spectrometers, DNA sequencing - have increased considerably in the last decade. Several studies show the potential of these bionanostructures for future stochastic biosensing technology. Stochastic biosensing is an approach that relies on the observation of individual binding events between analyte molecules and a single receptor. This approach is inherent to the organisms that use a single protein nanopore as a key element to start, manage and maintain the chemical and biophysical processes of living cells. Here, we discuss alpha-toxin as a bacterial exotoxin and prototype of a protein nanopore in real-time detection and characterization of molecules in aqueous systems.