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This paper presents an empirical analysis of two different methodologies for calculating national citation indicators: whole counts and fractionalised counts. The aim of our study is to investigate the effect on relative citation indicators when citations to documents are fractionalised among the authoring countries. We have performed two analyses: a time series analysis of one country and a cross-sectional analysis of 23 countries. The results show that all countries’ relative citation indicators are lower when fractionalised counting is used. Further, the difference between whole and fractionalised counts is generally greatest for the countries with the highest proportion of internationally co-authored articles. In our view there are strong arguments in favour of using fractionalised counts to calculate relative citation indexes at the national level, rather than using whole counts, which is the most common practice today.