This paper compares nationalism in the two ex-Czechoslovak countries—the Czech and Slovak republics. The aim is to analyze the measurement of nationalism in the 1995, 2003, and 2013 International Social Survey Program (ISSP) National Identity surveys. According to the nationalism measures from the ISSP survey – which are frequently used by authors analyzing nationalism—both countries experienced a significant rise in nationalism in the 1995 to 2013 period. Moreover, invariance testing of the nationalism latent variable confirms the possibility of comparing levels of nationalism between Czechia and Slovakia over time. However, the associations between nationalism, as measured in the study, and concepts related to nationalism—such as xenophobia, protectionism, or assertive foreign policy—suggest that what is measured as nationalism in 1995 is very different from what is measured in 2013. This is explained by a change of context which occurred in both countries between 1995 and 2013. While answering the same question had a strong nationalistic connotation in 1995, this was not the case in 2013. Based on our findings we advise against using the analyzed “nationalism” items as measurement of nationalism even beyond the two analyzed countries.