Radovan Karadzic's demeanour at The Hague is unlikely to satisfy his remaining admirers. A fantasist who entertained ideas above his station, he will be easily broken by the prosecution. Yet if Karadzic, the poetaster and quack healer, seems absurd, the ideology that he embodied was serious enough to have catastrophic and continuing effects.

Western diplomats and soldiers preferred to ignore the nature of the Greater Serbian programme that Karadzic and his colleagues implemented in the early 1990s. The reason is simple: that programme was manifestly and inherently genocidal. Had this been acknowledged, the agreed international strategy of neutrality would have been unsustainable. The principal intended victims of the programme were Bosnian Muslims. In the eyes of Serb propagandists, the Muslim population of Bosnia was doubly contemptible, both for their religion and because they were historically seen as renegade Serbs. Karadzic's deputy and then successor, Biljana Plavsic, has explained: “It was genetically deformed material [among the Serbs] that embraced Islam. And now, of course,” she lamented, “with each successive generation, this gene simply becomes concentrated. It gets worse and worse...” But a well-crafted final solution was at hand, and 100,000 Muslims paid the price of such “deformity” with their lives.

The attack on Bosnia's Muslims was thus also an attack on Islam, involving, for example, the wholesale systematic destruction of mosques. Indeed, Karadzic presented his policy in these terms. He urged the West to overlook Serb atrocities - which, at the same time, he denied - because his troops were defending Western interests. “It is amazing,” he protested, “that the US is aiding and abetting militant Islam.” This at the time was a lie. Bosnia's Muslims were not militants. They were by long tradition a brandy-swigging, pork-eating, easy-going Slavic people of very moderate religiosity. Yet through Karadzic's own actions the lie threatens to become self-fulfilling.

The early 1990s were formative in the rise of global Islamic terrorism, including what would be al-Qaeda, and Bosnia was central to this. In despair, the largely Muslim Sarajevo Government turned for support to Islamic groups and countries. Money and arms poured in - from among others, it seems, Osama bin Laden. There also arrived several thousand mujahideen, initially from Iran and Afghanistan, later from North Africa and the Middle East.

Distinguished by their bloodthirsty tactics rather than their military effectiveness, these foreign recruits were employed first against the Serbs and then against the Croats of central Bosnia in 1993, after the two former allies fell out. Their numerous crimes are still coming to light.

In different ways, both Karadzic and bin Laden now share an interest in propagating the idea that the wars in former Yugoslavia represented a titanic clash of civilisations. In the event, matters turned out somewhat differently. It was the intervention of America, the world's most explicitly Christian power, which in 1995 saved Bosnia. And in the Islamic world it was Turkey, the most explicitly secular Muslim-majority state, not the ayatollahs and jihadists, which did most to secure respect for Bosnia's statehood.

Karadzic's legacy is likely to prove more lasting than his poetry. The ethnically cleansed Bosnian Serb mini-state that he created has no plans to let non-Serbs back or to give up its aspiration to join Serbia. Of still greater moment, the Islamic reaction to Serb genocide will continue to complicate the West's defence against terrorism.

After the Dayton Accords, which in 1995 brought an end to the fighting - and to Karadzic's career - foreign mujahideen were meant to leave. But having obtained Bosnian citizenship, most eluded the requirement. Under US pressure, some of the most suspect were later removed, but many have stayed. Islamist hopes of a quick conversion of Bosnia's Muslims to extremism have so far been frustrated. But the conditions exist for it.

Huge sums of Saudi money have financed the building of new mosques, many of whose future imams are receiving training abroad, subject to radicalising Wahhabist influences. Within Bosnia, a network of foreign-based Islamic relief and educational foundations, charities and NGOs operates in the social space left by ineffective, corrupt government. Elsewhere, these have proved conducive for Islamist extremism and al-Qaeda. In any case, it is not necessary for most Bosnian Muslims to radicalise in order for Bosnia to become a base or gateway for terrorists.

This matters. With Croatia due to join the European Union in 2010, and with Serbia now likely to be offered early membership too, it is hard to see Bosnia being left behind in the rush. But the same European governments that watched as anti-Muslim fanatics destroyed the old Bosnia will now have to stop Islamist fanatics from turning the new one into a threat to the West.

Robin Harris is consultant director of Politeia and a former prime ministerial adviser to Margaret Thatcher

Times Recommends

• We have kit and leadership. Let’s go
• Behind the scenes at the biggest deal
• Conferences — what a waste of money