While diffusion tensor imaging based atlases in the brain are common, no muscle fibre atlases for the tongue have been created. An unbiased atlas was generated from ten healthy volunteers, by iteratively registering fibre orientation distributions calculated via constrained spherical deconvolution to a template. The atlas shows good reproducibility and better performance than an image intensity based atlas. Various tongue muscles can be detected in tractography of the atlas. This atlas may facilitate automatic segmentation of tongue muscles after tumour resection to evaluate impaired tongue function.