Crop diversity has an important role in sustainable agroecosystems. This study analyzed the crop diversity of agricultural holdings in particular regions (NUTS III) in Slovakia and identified the impact of Common Agricultural Policy (CAP) payments on the crop diversity of agricultural holdings. There are regional disparities in crop diversity in Slovakia. The highest crop diversity is typical for the regions with the best soil quality. From the results of econometric models, it was found that some of the CAP payments have an effect on crop diversity, mainly single area payment scheme (SAPS) payments, which had a negative effect, and payments for areas facing natural constraints (ANC) and animal welfare, which were found to have positive effects. It can be concluded that the second pillar of the CAP is able to improve or at least maintain crop diversity in Slovakia. Other important factors found to influence crop diversity are irrigation, total crop area corresponding with the farm size, geographical location including the soil quality, and the legal structure of agricultural holdings. However, the distance of the farm from the city, the education of managers, and membership in farmers’ associations are not important factors for crop diversity in Slovakia.