Fragments from lead ammunition pose a poisoning risk for predators like golden eagles that scavenge on non-retrieved carcasses or offal left behind by hunters. Three golden eagles were found in the Swiss Alps with an acute lead poisoning. To investigate whether the few cases of lead-poisoned golden eagles are exceptional events or whether a substantial proportion of the Alpine golden eagle population is affected by lead at sublethal levels, we measured body burdens in golden eagles from Switzerland in comparison to eagle owls from the same area and to their respective prey. These two raptor species differ in their food as eagle owls feed on live-caught prey. Lead levels in soft tissues were significantly higher in golden eagles (median 1.14 μg g−1 dry weight in liver, 0.99 μg g−1 in kidney) than in eagle owls (0.14 and 0.23 μg g−1). Bones of golden eagles contained 10 times more lead (median of 12.45 μg g−1 dry weight) than owl bones (1.28 μg g−1), which represent substantially higher levels than previously reported for golden eagles. Bones of prey of both golden eagles and eagle owls had low lead concentrations. In order to investigate whether the sublethal lead of golden eagles originates from ammunition or from generic environmental contamination, we examined lead isotope ratios. Lead isotope signatures of golden eagle bones were very similar to those of ammunition, but differed from the signatures of bones of their prey, eagle owls and soil. Isotope signatures did not change with increasing bone lead concentration in golden eagles or any other group examined. These findings indicate that in the Alps, most golden eagles take up lead from spent ammunition in carcasses or their offal in sublethal quantities throughout their life and a few in lethal quantities leading to acute lead poisoning.