We explore the effects of event-by-event fluctuations of Hanbury Brown–Twiss (HBT) radii and show how they can be observed experimentally. The relation of measured HBT radii extracted from ensemble-averaged correlation functions to the mean of their event-by-event probability distribution is clarified. We propose a method to experimentally determine the mean and variance of this distribution and test it on an ensemble of fluctuating events generated with the viscous hydrodynamic code VISH2+1. Using the same code, the sensitivity of the mean and variance of the HBT radii to the specific QGP shear viscosity η/s is studied. We report sensitivity of the mean pion HBT radii and their variances to the temperature dependence of η/s near the quark-hadron transition at a level similar (10–20%) to that which was previously observed for elliptic and quadrangular flow of charged hadrons [1].