Background We undertook diffusion tensor imaging analysis of brainstem fiber tracts in two Joubert syndrome patients. Methods Two Joubert syndrome patients underwent magnetic resonance imaging brain examination with diffusion tensor imaging. Imaging findings were compared with five age- and sex-matched control subjects with approval from the institutional ethic committee. The medical history and clinical examination findings in both patients were documented. Results Diffusion tensor imaging analysis of the first patient demonstrated absence of the dorsal pontocerebellar tract and thinning of the middle cerebral peduncle. Diffusion tensor imaging analysis of the second child revealed thinning of the both the dorsal pontocerebellar and ventral pontocerebellar tract. Both patients exhibited thickened and horizontally oriented superior cerebellar peduncles. The superior cerebellar peduncles also failed to decussate in the mesencephalon. Conclusion Pontocerebellar tract abnormalities in Joubert syndrome patients have not been previously recognized. The difference in the pontocerebellar tract between the two Joubert syndrome patients suggests a spectrum of severity of pontine axonal migration abnormality.