The US admitted to losing 1 F-16 and 1 F-117 to SAM. Serbia, at various times during the conflict, claimed that they had shot down as many as 10-20 aircraft. However it's also suspected that some of these aircraft were drones/UAV's, or Serbia's own aircraft.
"When the NATO attack finally came, on the evening hours of 24 March 1999, the MiGs went into action, being scrambled one after the other. The two fighters that took off from Nis and were vectored to intercept targets over southern Serbia and Kosovo, were swiftly dealth with by NATO fighters: the MiG-29 flown by Maj. Dragan Ilic was damaged - either by an AIM-120 fired from a Dutch F-16AM fighters, or by a Serbian SA-6 SAM, in a case of fratricide fire."
"After a pause of almost a month, on 4 May finally Lt.Col. Milenko Pavlovic scrambled on MiG-29 to intercept a NATO strike in the area of Valjevo, his home-town, which the previous night was first hit by an earthquake and then by a heavy NATO-strike. Appearing too late on the scene and experiencing one malfunction of the weapons and navigation systems on his aircraft after the other, Lt.Col. Pavlovic was eventually intercepted by two USAF F-16Cs. Both US fighters were flying on the end of the NATO-formation, and had to be turned around by the E-3 Sentry AWACS aircraft in order to engage – while simultaneously also attacked by the Serbian air defence units. Lt.Col. Pavlovic was shot down within a short period of time, and killed. Even if the Serbs subsequently found fragments of a Strela-2M MANPAD in the wreckage of his MiG, this kill was officially credited to a USAF pilot from the 78th FS."
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The Serbian AF was known to use their MiG's with ground-based SAM traps against NATO aircraft. Unfortunately for them, the electronics/IFF system on the MiG-29's were in a poor state that one Serbian pilot commented "Every night I've flown I've seen a SAM shot at me or one of my wing mates".