Diffusion tensor imaging has been useful in demonstrating non-decussating corticospinal tract (CST) and superior cerebellar peduncles (SCP) in Joubert syndrome (JS) related disorder and in horizontal gaze palsy with progressive scoliosis (HGPPS). However, measurements of fractional anisotropy (FA) and mean diffusivity (MD) have never been performed in these diseases. The aim of our work was to investigate if FA and MD values in uncrossed white matter bundles due to defective axon guidance are different from normal decussating fibers. Two patients with HGPPS and four with JS were included. FA and MD were measured by region of interest manually placed on the CST, the SCP and the posterior rows (PR) of the pons. The same measurements were performed in 59 control patients. Comparison of these values between patients and controls was performed by graphical inspection. MD values were normal in all cases. In all patients with HGPPS and JS, FA measurements in SCP were not different from normal controls. FA values in PR and in CST were not different in JS patients but higher than in controls in HGPPS patients. This difference was statistically significant. Normal MD values seem to indicate that MD and FA values likely represent two very different processes in the developing brain. High FA values in PRs and CST in HGPPS, implicating microscopic deficits of axonal structures, is a unique finding in this disease. Abnormal measurements on PR confirm a role of these fibers in the pathogenesis and clinical presentation of HGPPS.