Horizon Europe has a pillar structure.

The first pillar focuses on excellent science, namely European Research Council (ERC) projects and Marie Skłodowska-Curie actions (MSCA networks for doctoral students, MSCA individual grants for postdoctoral students, MSCA exchanges, MSCA COFUND and MSCA and citizens). Research infrastructures are also part of this pillar.

The second pillar focuses on the global challenges and competitiveness of European industry. In addition to the Joint Research Center (JRC), this pillar brings together six broad thematic clusters that represent areas of global challenge (rather than sectoral targeting). The specific priorities of each cluster are divided into so-called areas of intervention. These are the following clusters and areas:

• Health (Lifelong health; Environmental and social health factors; Non-communicable and rare diseases; Infectious diseases; New tools, technologies and digital solutions for healthcare; Healthcare systems)
• Culture, Creativity and Inclusive Society (Democracy and Governance; Cultural Heritage; Socio-Economic Transformation)
• Civil Security for Society (Disaster-resistant companies; Protection and security; Cyber ​​security)
• Digital, Industry and Space (Manufacturing Technology; Key Digital Technologies; Advanced Materials; Emerging Breakthrough Technologies; Artificial Intelligence and Robotics; Next Generation Internet; Advanced Computing and Large Volume Data; Circulating Industry; Low Carbon and Ecological Industry; Space, Including Earth Observation)
• Climate, Energy and Mobility (Climate science and solutions; Energy supply; Energy systems and networks; Buildings and industrial facilities in energy transformation; Municipalities and cities; Competitiveness of transport industry; Clean, safe and accessible transport and mobility; Intelligent mobility; Energy storage)
• Food, Bioeconomy, Natural Resources, Agriculture and Environment (Environmental observation; Biodiversity and natural resources; Agriculture, forestry and rural areas; Seas, oceans and inland waters; Food systems; Innovation systems based on biotechnology in the EU bioeconomy; Circulatory systems)

The pillar will also include five missions with clearly defined ambitious goals.

The third pillar deals with the concept of an innovative Europe. This pillar includes the European Innovation Council (EIC), whose main tools are EIC Pathfinder, EIC Transition and EIC Accelerator. It also includes the European Institute of Innovation and Technology (EIT) and the topic of European innovation ecosystems.

An important emphasis for the Czech Republic should be projects that are part of the section on widening participation and strengthening the ERA. The EC sees the widening of participation as an opportunity for the EU-13 countries to participate as much as possible in the Horizon Europe FP projects, thus strengthening their position in the ERA. The main tools are mainly TEAMING, TWINNING, ERA Chairs.