Despite their importance for brain function, cortico-subcortical white matter tracts are under-represented in diffusion MRI tractography studies. Their non-invasive mapping is more challenging and less explored compared to other major cortico-cortical bundles. We introduce a set of standardised tractography protocols for delineating tracts between the cortex and various deep subcortical structures, including the caudate, putamen, amygdala, thalamus and hippocampus. To enable comparative studies, our protocols are designed for both human and macaque brains. We demonstrate how tractography reconstructions follow topographical principles obtained from tracers in the macaque and how these translate to humans. We show that the proposed protocols are robust against data quality and preserve aspects of individual variability stemming from family structure in humans. Lastly, we demonstrate the value of these species-matched protocols in mapping homologous grey matter regions in humans and macaques, both in cortex and subcortex.