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The effect of uncertainties regarding modelling choices and knowledge of specific structural configurations on the seismic vulnerability evaluation of masonry buildings in Slovenia were studied using two case studies: a set of damaged buildings from the rural area of NW Slovenia hit by earthquakes in 1998 and 2004 and the urban buildings from the historic city centre of Ljubljana. Two modelling strategies were applied-failure mechanisms analysis by means of macro element methodology (MEM) and non-linear response analysis by means of structural element modelling. The accuracy in predicting failure modes by MEM ranged between 50 and 80 % of the stock of building in rural area. The most critical failure mechanisms were due to out-of-plane loading. Given the uncertainties associated with the data relative to the urban architecture stock, the MEM analysis was carried out considering different hypotheses, leading to a range of 30-70 % damaged buildings, for 475 years return period, with diverse failure mechanisms and ultimate capacity depending on specific structural assumptions. For one building of rural architecture already damaged during previous earthquake in 2004, where due to the extensive in-situ campaign the influence of uncertainties were minimised, direct comparison of the effectiveness of both methods were investigated. MEM assessment yields more conservative results in respect to non-linear approach and thus may be an efficient tool for the design of strengthening measures for heritage buildings to prevent damage in lower intensity events with higher probability of occurrence. [ABSTRACT FROM AUTHOR]