Congenital ocular motor apraxia (COMA) occasionally shares with Joubert syndrome (JS) and related disorders (JSRDs) a peculiar malformation, the ‘molar tooth sign’ (MTS). In JSRDs, the absence of superior cerebellar peduncles (SCP) decussation is reported. To investigate whether COMA demonstrates similar abnormal axonal pathways. Eight healthy age-matched controls, three children with clinical COMA and one child with clinical JSRD underwent examination with a 1.5-T MRI scanner. Diffusion-weighted imaging (DWI), colour-coded fractional anisotropy maps and three-dimensional diffusion tensor imaging (DTI) tractography of the cerebellorubral network were analyzed. On DTI cartography, the ‘red dot’ originally supposed to represent the SCP decussation in the midbrain was present in controls as well in those with COMA but absent in the single case with JS. In none of the subjects including controls was 3-D FT able to depict the SCP decussation. When seeded, the red dot resulted in the ventral tegmental decussation (VTD). It was normal in controls and in patients with COMA but was absent in our single patient with JSRD. MTS was identified in alla patients with COMA and in the patient with JSRD. MTS can be present in both COMA and JSRD but the underlying anatomy depicted by fibre tracking is distinct. The main difference is the integrity of the VTD in COMA.