The aim of this study was to locate foraminal, shape, and cribrosity features in the skull of chinchillas (Chinchilla laniger) and determine whether the hypertrophic defect of teeth affects variation in these features. Examinations were carried out on 56 adult skulls from the Natural History Museum in London and 300 skulls from farm animals. Altogether, 10 basic measurements of the cranium and mandible length, breadth, and height were taken as well as 29 monolateral and bilateral foraminal, shape, and cribrosity features, so called epigenetic traits, were located. Average values and standard deviations were calculated for metric traits, as well as average values for non-metric trait ranks, medians, and modes, and minimum and maximum rank values. Out of 29 epigenetic traits, 18 differed significantly of which 10 were localised on the cranium and 8 on the mandible. For six foraminal, cribrosity, upper dental row length, mandibular length and braincase height traits, the values of simple correlation coefficients showed no association or weak or moderate relationship in all skull groups examined. These findings can be a basis for next studies on developmental disorders in the early epigenesis of long-tailed chinchilla and may be used for the identification of the factors generating these abnormalities.