Despite the importance of short association fibres (SAF) for human brain function, their structures remain understudied. It is not known how SAF are organised across the brain, and how consistent their geometries and locations are across individuals. To address this gap, we mapped the precise structures of SAF in the primary (V1) and secondary (V2) visual cortex in a group of participants in vivo and a post mortem specimen. We assessed the consistency of SAF geometries and their expected structural and functional topography using probabilistic tractography on sub-millimetre-resolution diffusion-weighted MRI combined with functional MRI retinotopic maps in vivo . We found that dense SAF connected V1 and V2, forming sheet structures with retinotopic topography and bearing consistent geometries that resembled the local V1–V2 cortical folding. In vivo findings were corroborated by the robust and fine-grained post mortem reference. Our in vivo approach provides important insights into SAF organisation and could be applied to studies across species on cortical and SAF reorganisation and support neuronavigation.