We used genotype data across 18 microsatellite loci to establish the paternity of giant panda cubs at the Chengdu Zoo and the Chengdu Research Base of Giant Panda Breeding. The results demonstrate that the combined exclusion probability using these 18 microsatellite loci is 0.999921 while confidence is 95 % when the mother is known; if mother is unknown then the exclusion probability is 0.994109, but the confidence of this is less than 80%. Since the mother-offspring relationship is known in captive populations, the results could resolve unknown paternities in the Chengdu ex situ populations. However, to establish accurately the genetic relationships of wild giant pandas,more microsatellite loci may be required.