Uncertainties regarding the influence of modelling strategies for the evaluation of seismic vulnerability of masonry buildings in Slovenia were studied on two case studies- damaged buildings from the rural area of NW Slovenia hit by earthquakes in ʼ98 and ʼ04 and the urban buildings from the old city centre of Ljubljana. Two strategies were applied - failure mechanismsanalysis by means of FaMIVE methodology and non-linear response analysis by means of storey and global response (SREMB and 3Muri). The accuracy in predicting failure modes by FaMIVE was 50% considering the stock of investigated building in rural area. The most critical failure mechanisms were due to out-of-plane loading. For urban architecture, in-plane failure dueto weak spandrels was the predominant one. The mechanism assessment yields more conservative results in respect to non-linear approach and thus may be anefficient tool for the design of strengthening measures for heritage buildings to prevent damage in lower intensity events with higher probability of occurrence