Over the past two decades, Moral foundations theory (Haidt & Joseph, 2004) has increasingly become a leading theory in the field of moral psychology. According to this theory, there are five basic moral foundations: care, fairness, loyalty, authority, and sanctity. In addition, there are also higher-level foundations: individualizing foundations (including care and fairness) and binding foundations (including authority, loyalty, and sanctity). To examine individuals’ acceptance of different types of moral foundations, the Moral Foundations Questionnaire (Graham et al., 2011) was developed and originally validated in the U.S. population and later in other samples around the world. Results show that in some samples, the appropriate five-factor structure consists of basic moral foundations, while in others, the appropriate two-factor structure consists of higher-order foundations. Considering the cross-cultural sensitivity of measuring moral dimensions, the main objective of this study is to investigate the appropriateness of the two factor structures of the Moral Foundations Questionnaire on a Croatian sample (two-factor and five-factor structure). The study included 433 participants with a mean age of 21.72 (SD = 4.1) years. In addition to demographic data, political orientation, and level of religiosity, participants completed the Moral Foundations Questionnaire and the Attitudes Toward Homosexuality Scale to examine criterion validity. A confirmatory factor analysis was conducted to determine the most appropriate model of the Moral Foundations Questionnaire for the Croatian population. The results show that the originally proposed five-factor structure (care, fairness, loyalty, authority, and sanctity) is not suitable, while the two-factor structure (individualizing and binding) with high reliability coefficients for both dimensions proved to be more suitable for use in the Croatian sample. The results suggest that the Moral Foundations Questionnaire should be considered as a two-factor structure and is suitable for future measurements of moral foundations in the Croatian sample.