Aragonite is the normal form of calcium carbonate found in teleost otoliths, but it is sometimes replaced by vaterite, an alternate crystalline structure. We investigated the assumption that sagittal otoliths with vaterite replacement were unique to stocked lake trout Salvelinus namaycush in the Laurentian Great Lakes. Earlier studies had attributed these abnormalities to stocking stress, and proposed that the presence of vaterite could separate individual unmarked stocked lake trout from their wild counterparts. We examined and described the frequency of vateritic sagittae in two wild and three stocked populations of lake trout from the Great Lakes and a wild population from a remote inland lake in northern Canada. Among lake trout caught 2–12 years after being stocked, prevalence of vateritic sagittae was 66% for Lake Superior fish, 75% for Lake Huron fish, and 86% for Lake Ontario fish. Among wild fish caught, vateritic sagittae were present in 37% of Lake Superior fish, 22% of Lake Huron fish, and 49% of northern Canada fish. We also compared year-to-year differences in prevalence in four year-classes of fingerling lake trout reared in two U.S. national lake trout hatcheries. Prior to release, between 53 and 84% of the hatchery fish had at least one vateritic sagitta, and prevalence increased with handling associated with hatchery practices. Vateritic sagittae in wild fish might also indicate stress in nature. The presence of vateritic sagittae in both wild and stocked fish compromises the use of this characteristic as an unequivocal indicator of a particular fish's origin. Among-population differences in both the prevalence and the extent of vaterite replacement, however, may provide a means of differentiating between stocks of sympatric unmarked wild and stocked lake trout.