In the present study a comparative morphometric analysis of sagittal otoliths was performed in three Channichthyids (Pseudochaenichthys georgianus, Chaenocephalus aceratus and Chaenocephalus gunnari) collected during a research survey carried out between January 23 and February 13, 2016, along the continental shelf and slope around Elephant Island (Subarea 48.1) and the South Orkney Islands (Subarea 48.2). Morphometric analysis was addressed using Basic size descriptors (BSD; area & perimeter), shape indices (SI; circularity, squareness and roundness) and elliptical Fourier Descriptors (EFD) on 2D binarized images of left and right otoliths for fish ranging from 20 to 67 cm TL. To test for significant differences between the left and right sagittae in BSDs, a univariate and multivariate ANOVA and MANOVA were used, with BDSs as dependent variables and otolith type as fixed factor. ANOVA and MANOVA showed all standardized BSDs did not varied significantly between right and left sagittae (P>0.05). All EFDs derived from the 20 harmonics analyzed were homoscedastic and normal, and showed very low level of correlation among them. Hence, all coefficients were used in MANOVA and LFDA. MANOVA showed significant differences in the contour between both otolith pairs for each species (p<0.001). Similarly, EFS coefficients showed a high discriminatory power to distinguish the left and right otoliths, with a total percentage of correct classification of 76, 96, and 89% for P. georgeanus, C. gunnari and C. aceratus. A link between the extreme environmental conditions of Antarctic waters and the occurrence of the unusual high asymmetry in the otolith contour is proposed for Channichthyids and its implications are discussed.