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This article shows the changes in the populations of Croatian and Serbian ethnic affiliation in Croatia based on population censuses of 1991 and 2001. In the last intercensal period (1991-2001), methodological definitions of resident population changed significantly, Croatia's administrative-territorial borders changed and a war occurred (1991-1995), all of which influenced the demographical situation of Croatia. It is of special importance that the term 'ethnic affiliation' is significantly unstable and unpredictable and highly influenced by both subjective and external influences, which make its analysis even more difficult. By establishing a connection between the old (1991) and the new (2001) names of settlements, the authors demonstrated the changes in the share of ethnic Croats and Serbs in the total population of towns and municipalities in Croatia in the observed intercensal period. Both the demographic and the ethnic profile of Croatia changed in the period of 1991-2001. The total population of Croatia, as well as the population of ethnic Serbs, decreased in this period, while the population of ethnic Croats increased. Since Croatia had a negative natural increase in the observed period, this increase is attributed to migrations and changes in declarations of ethnic affiliation. While the share of ethnic Serbs decreased significantly (from 12,2% in 1991 to 4,5% in 2001), their territorial distribution remained practically the same. .