This paper presents a description and comparison of the Nazlet Khater 2 (NK 2) inner ear structures. This specimen is the only complete modern human skeleton from the earliest Late Stone Age in Africa. The interest in the inner ear structures lies with their strong genetic component. The morphology and biometrical characteristics of the NK 2 bony labyrinth are described and compared to extant modern humans, Middle and Upper Paleolithic modern humans, and Neanderthal specimens by means of uni-, bi-, and multivariate analyses. The NK 2 inner ear presents particular features that are unusual within our extant modern human sample, but that occur more frequently among Upper and Middle Paleolithic modern human specimens. In addition, the two latter comparative groups fall on the edge of extant human variation in the multivariate morphological analysis. These results suggest that Late Pleistocene modern human variation differs from that of recent humans. Finally, the similarities between NK 2 and the Upper Paleolithic sample, suggested by the discriminant analysis, may indicate a close relationship between this Nile Valley specimen and European Upper Paleolithic modern humans.