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The U.S. flew in the Mujahideen, as it was no skin off its back if those mutilating fighters whacked off the heads of Serbian farmers. The Dutch Srebrenica report highlighted the "enormous" amount of weapons and middle eastern fighters brought in by the Pentagon:

America used Islamists to arm the Bosnian Muslims
The Srebrenica report reveals the Pentagon's role in a dirty war
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Bill Clinton and the Pentagon were keen to be seen as creditworthy and repaid in the form of an Iran-Contra style operation - in flagrant violation of the UN security council arms embargo against all combatants in the former Yugoslavia.
The result was a vast secret conduit of weapons smuggling though Croatia. This was arranged by the clandestine agencies of the US, Turkey and Iran, together with a range of radical Islamist groups, including Afghan mojahedin and the pro-Iranian Hizbullah. Wiebes reveals that the British intelligence services obtained documents early on in the Bosnian war proving that Iran was making direct deliveries.
Arms purchased by Iran and Turkey with the financial backing of Saudi Arabia made their way by night from the Middle East. Initially aircraft from Iran Air were used, but as the volume increased they were joined by a mysterious fleet of black C-130 Hercules aircraft. The report stresses that the US was "very closely involved" in the airlift. Mojahedin fighters were also flown in, but they were reserved as shock troops for especially hazardous operations.
Light weapons are the familiar currency of secret services seeking to influence such conflicts. The volume of weapons flown into Croatia was enormous, partly because of a steep Croatian "transit tax". Croatian forces creamed off between 20% and 50% of the arms. The report stresses that this entire trade was clearly illicit. The Croats themselves also obtained massive quantities of illegal weapons from Germany, Belgium and Argentina - again in contravention of the UN arms embargo. The German secret services were fully aware of the trade.
Rather than the CIA, the Pentagon's own secret service was the hidden force behind these operations. The UN protection force, UNPROFOR, was dependent on its troop-contributing nations for intelligence, and above all on the sophisticated monitoring capabilities of the US to police the arms embargo. This gave the Pentagon the ability to manipulate the embargo at will: ensuring that American Awacs aircraft covered crucial areas and were able to turn a blind eye to the frequent nightime comings and goings at Tuzla.
Weapons flown in during the spring of 1995 were to turn up only a fortnight later in the besieged and demilitarised enclave at Srebrenica. When these shipments were noticed, Americans pressured UNPROFOR to rewrite reports, and when Norwegian officials protested about the flights, they were reportedly threatened into silence.