Knowledge of anatomical variations in the base of the skull and anatomical landmarks is crucial for clinical procedures by surgeons, ENT physicians, and radiologists. This study investigated morphometric and anatomical variations in the foramen magnum, occipital condyles, hypoglossal canals, and jugular foramina to improve knowledge of the base of the skull’s complex anatomy and consider the anatomical variations via a morphometric study. One hundred and sixty intact skulls were investigated. Morphometric measurements showed that the foramen magnum, occipital condyles, hypoglossal canals, and jugular foramina were all significantly larger in males than females and could be useful for sex determination. Increased awareness of morphological location and anatomical landmark variation can improve surgical proficiency.