The aim of this paper is efficiency assessment of railway companies from larger Europe during the most recent time period, taking into account different input-output configurations. For this aim, two-stage analysis is employed, where efficiency scores are obtained by DEA in the first stage, while in the second stage different statistical tests are conducted and Tobit analysis is used in order to evaluate influence of different environmental factors. It has been found that railways were oriented either on passenger or freight transportation, with only few companies demonstrating high performance in both modes. While companies from Western Europe showed higher performance than companies from Central and Eastern Europe regarding passenger and overall transportation, this is not the case concerning freight transportation. Except for few companies, there are no clear trends in performance during the period observed, in terms of constant efficiency level increase or decrease. Great impact of factors selection on results has been identified.