This is a historic moment for Europe. When ten countries in central and eastern Europe (including Malta and Cyprus) join the European Union (EU) this week, the old continent will reach a level of integration that the EU's founding fathers could only have dreamt of in the 1950s. But will it also be a historic day for European research? Up to a point. After all, the EU will gain tens of thousands of scientists. But a look at the recent past highlights the enormous challenges to be faced.

In the hardship that followed the fall of communism, science in central and eastern Europe came close to extinction. As recently as 2000, when Nature held a meeting in the former East German city of Dresden on the perspectives of science in the region, the survival of many post-communist science communities was hanging by a thread. Isolation, paltry salaries and funds, obsolete laboratories and lack of equipment were pervasive problems. Liberty, it seemed, had also brought poverty.

That science did not collapse was due to a strong determination to survive, good improvizational skills and considerable western aid. Furthermore, researchers in the new member states have been eligible to participate in the EU's Framework Programmes of Research since 2002. In the past few years, a number of EU-funded centres of excellence — in fields from molecular biology to materials research, social sciences and humanities — have been set up across the region, from Tartu in Estonia to Ljubljana in Slovenia.

But although the transition process in the new EU member states has gathered pace, strong universities and research institutes there are still few and scattered. Progressive science managers in Warsaw, Prague, Budapest and elsewhere have invested in better conditions for competitive research, including peer-reviewed grant agencies, a stronger role for university research and collaborations with western groups and organizations. But the speed of change is limited by scarce funds and by the inertia of senior scientists who are unwilling to adapt.

Poland, which alone accounts for half of the 120,000 researchers who will now become EU citizens, currently has the fastest annual growth in gross domestic product (GDP) in Europe. But its total research expenditure has fallen in real terms over the past few years. Even worse, a legacy of under-performing institutes and ‘industrial labs’, employing more than 10,000 researchers, continues to produce poor results. Domestic funding is proportionately better in smaller countries, such as the Czech Republic, Slovakia and Hungary. But given the relative weaknesses in the east, the EU as a whole will fall further behind schedule in achieving its nominal goal of spending 3% of GDP on science by 2010.

The biggest obstacle is the short-sightedness of governments who tend to invest in areas that promise immediate returns. Scientists in the east do not stand to benefit as they should from the tens of billions of euros in structural funds — the EU's subsidies to poorer regions — that will now flow into the new member states. Research managers in Brussels would like to see more of this money being spent on capacity-building in research, but the EU has little control over its deployment. This should change. A historic period of enlargement is an appropriate time for European citizens' taxes to be spent in a more far-sighted fashion.