On 11 December 2025, the European Commission, the European Parliament and the Council of the European Union reached a political agreement on a comprehensive reform of the EU pharmaceutical legislation.
For people living with a rare disease—and for the researchers, clinicians and developers working to expand treatment options—these changes matter because they set the rules for how evidence is assessed, how incentives for orphan and paediatric medicines are structured, and how shortages are prevented and managed. This is a policy moment ERDERA partners are watching closely as it may affect the wider environment for rare disease clinical research and translation.
What has been agreed so far
The reform began with a Commission proposal in April 2023 and has moved through positions adopted by the European Parliament (April 2024) and the Council (June 2025). The package consists of a new Directive and a new Regulation, which together will update the regulatory framework for medicines in the EU, including those intended for rare diseases and children.
According to the European Medicines Agency (EMA), this is the most significant overhaul of the EU medicines framework in over two decades. EMA also notes that the political agreement is still subject to legal checks and formal approval by the European Parliament and the Council.
EMA’s Executive Director Emer Cooke described the deal as “a historic milestone … for patients across the EU”, highlighting an emphasis on scientific rigour alongside measures intended to improve efficiency and support innovation.
What to watch for rare disease and paediatric medicines
While the final legal texts will be detailed in 2026, the agreement signals several areas that are particularly relevant for orphan and paediatric development.
Changes to EMA processes and timelines. EMA has indicated that the reform is expected to simplify its scientific committee structure for human medicines and reduce assessment timelines for marketing authorisation opinions from 210 to 180 days, alongside wider moves towards electronic submissions and electronic product information. These measures may affect how quickly developers can progress through EU-level evaluation—an issue of direct relevance where patient populations are small and time matters.
Paediatric development. EMA has highlighted work to formalise a more iterative approach to paediatric investigation plans (PIPs), building on pilots already run by the Agency. For developers of orphan medicines—where early evidence can be limited—clarity on how paediatric requirements can be agreed and updated over time will be important.
Orphan incentives and “breakthrough” orphan medicines. The European Parliament’s background note on the provisional agreement sets out (as a non-exhaustive selection, and subject to revision) a proposed framework covering orphan designation and market exclusivity, including references to “breakthrough orphan medicinal products” and differentiated exclusivity durations in certain circumstances. The detail—and any specific implications for rare disease portfolios—will depend on the final adopted text and guidance.
ERDERA partner Fondazione per la Ricerca Farmacologica Gianni Benzi has followed the legislative debate and will continue to monitor developments as the package moves towards formal adoption and implementation.
Critical Medicines Act: a parallel track focused on supply security
Alongside the “pharma package”, the Commission has proposed a Critical Medicines Act, intended to strengthen availability and security of supply for essential medicines in the EU and to improve resilience against shortages. The Council’s public overview explains how the proposal is designed to complement the wider reform of EU pharmaceutical legislation and focuses on practical measures such as supply chain resilience and production capacity.
Timeline and where to follow updates
EMA has published a dedicated implementation “gateway” page with an indicative timeline and will update it as work progresses: Reform of the EU pharmaceutical legislation (EMA). EMA notes that the adopted acts are expected to enter into force in 2026, followed by a transition period running to 2028, when the new pharmaceutical legislation is expected to become applicable.
As the final texts and guidance become available, the practical impact for rare disease and paediatric medicines should become clearer—particularly on incentives, evidence expectations, and how new procedural flexibilities will work in practice for small populations and advanced therapies.
