Corynebacterium bovis (Cb), the etiology of Corynebacterium associated hyperkeratosis (CAH) in nude mice, may impact research outcomes. Little is known about the differences in the course and severity of CAH in different outbred athymic nude mice stocks. Three genetic stocks (designated A, B, and C), 1 of which was obtained from 2 geographically separate colonies with distinct microbiota (A1 and A2), were inoculated topically with 1 x 10^8 CFUs of a pathogenic Cb field isolate (#7894; n = 6/stock) or sterile media (n=2/stock; controls). Clinical signs were assessed daily and scored 0 to 5 based on lesion severity. Mice were euthanized at 14 (A1, A2, B, and C) or 28 (B) days post inoculation (dpi), macroscopic changes documented, and 6 skin samples per mouse were obtained and histologically scored 0 to 4 based on the presence and severity of hyperkeratosis, acanthosis, inflammation, and bacterial colonies. No stock A1 or control mice developed clinical disease; 1 of 6 stock B mice developed mild CAH (mean peak clinical score [MPCS] of 0.33) at 14 dpi (14 day group) and 2 of 6 stock B (28 day group) developed mild CAH at 15 dpi (MPCS of 0.33); and, all stock C and A2 mice developed significant clinical signs at 5 dpi (MPCS of 2.5 and 3, respectively) which resolved by 11 dpi. Despite differences in clinical presentation, all Cb-infected mice had hyperkeratosis and/or acanthosis with associated bacterial colonies. Stocks A1 and B, which had minimal or no clinical signs, were colonized with Corynebacterium amycolatum (Ca). In contrast, stocks C and A2 were not colonized with Ca, raising the possibility that Ca and/or other components of the skin microbiota may mitigate clinical signs but not necessarily all histopathologic changes associated with infection. These findings suggest host genetics and/or the skin microbiota can markedly influence the presentation of CAH in nude mice.