Since regaining independence, Latvia and Estonia have carried out education reforms aimed at adjusting the education system to the requirements of a multicultural society and at putting in order the general education system of minorities. This investigation analyzes the results obtained in the ICCS 2009 study, comparing the understanding and opinions the 14 year old students in Estonia and Latvia have about their country, their sense of European identity and belonging in relation with the achievement in the citizenship education test as well as the achievement in the European module test on the European Union. The authors investigate the Latvian and Estonian data from ICCS 2009 and its regional European module regarding the aspect of the state language and the Russian language, and determine the relation between the students’ opinions and their test achievement. The opinion of students from schools with the state language of instruction differed considerably from the opinions expressed by students learning in the minority education programs where the language of instruction is Russian. On the whole, the results of the study showed that many students from the minority programs with the Russian language of instruction in Latvia and Estonia have lower loyalty sense to their country.