Rural development policy in the European Union (EU) has been implemented through different instruments. This paper is focused on support for the forestry sector from the EU funds in the years 2004–2006 in two EU Member States – Czech Republic (CZ) and Slovakia (SK). The comparison of support for forestry activities from the EU funds, delivered through the implementation of National Operational Programmes, showed differences at country level. Both countries had the opportunity to apply for support based on common EU policy, but they were able to select measures that reflected their specific needs and priorities at national level. Within Operational Programmes the following indicators were evaluated: description of forestry measures, financial support, number of applications, beneficiaries, outcomes and impacts. The comparison of financial support showed that the greater part of support in SK was granted to non-profit investments, whereas in CZ into profit making investments. The main difference was in the interest shown by applicants for support. In CZ nearly 80% of submitted applications were approved compared to 59% in SK. The analysis showed that the main reason for differences in utilisation of available sources was that different principles were applied when selecting supported measures or defining the activities to be supported within the measure.