The Leiden Ranking 2011/2012 is a ranking of universities based on bibliometric indicators of publication output, citation impact, and scientific collaboration. The ranking includes 500 major universities from 41 different countries. This paper provides an extensive discussion of the Leiden Ranking 2011/2012. The ranking is compared with other global university rankings, in particular the Academic Ranking of World Universities (commonly known as the Shanghai Ranking) and the Times Higher Education World University Rankings. The comparison focuses on the methodological choices underlying the different rankings. Also, a detailed description is offered of the data collection methodology of the Leiden Ranking 2011/2012 and of the indicators used in the ranking. Various innovations in the Leiden Ranking 2011/2012 are presented. These innovations include (1) an indicator based on counting a university's highly cited publications, (2) indicators based on fractional rather than full counting of collaborative publications, (3) the possibility of excluding non-English language publications, and (4) the use of stability intervals. Finally, some comments are made on the interpretation of the ranking and a number of limitations of the ranking are pointed out.