Seismic assessment of existing masonry structures requires a numerical model able to both reproduce their nonlinear behaviour and account for the different sources of uncertainties; the latter have to be dealt with since the unavoidable lack of knowledge on the input parameters (material properties, geometry, boundary conditions, etc.) has a relevant effect on the reliability of the seismic response provided by the numerical approaches. The steadily increasing necessity of combining different sources of information/knowledge makes the Bayesian approach an appealing technique, not yet fully investigated for historic masonry constructions. In fact, while the Bayesian paradigm is currently employed to solve inverse problems in several sectors of the structural engineering domain, only a few studies pay attention to its effectiveness for parameter identification on historic masonry structures. This study combines a Bayesian framework with probabilistic structural analyses: starting from the Bayesian finite element model updating by using experimental data it provides the definition of robust seismic fragility curves for non-isolated masonry towers. A comparison between this method and the standard deterministic approach illustrates its benefits. This article is part of the theme issue 'Environmental loading of heritage structures'.