Metatarsal fractures often occur around the diaphyseal nutrient foramina (NF) which vary in topography depending on population affinity. Topographical and morphometrical knowledge of the NF is crucial in understanding fracture development and fracture site healing patterns. The current study aimed to describe the topography and the morphometry of the metatarsal diaphyseal NF in South African Africans (SAA), South Africans of European descent (SAED) and South Africans of Mixed Ancestry (SAMA). The study examined 4284 dry cadaveric metatarsals from both sexes and sides of these populations for NF topography and morphometry, including the presence, number, location, position, size and direction of the NF on the metatarsal bones. The NF was present in 99.4% of the metatarsals. Most (84.5%) metatarsals examined had a single NF. Most (97.4%) NF were located in the middle third of the metatarsal bones. The median foramina index (FI) of the second metatarsal exhibited population affinity and significant differences were found both on the left second metatarsal (P = 0.043), and the right second metatarsal (P = 0.046). The position of NF was predominantly lateral on the first (92.4%), second (64.9%) and third (59.1%) metatarsals, whilst the position was predominantly medial on the fifth (65.1%) metatarsals. The NF positions on the fourth metatarsals showed the greatest population variability. The first metatarsals had primarily dominant-sized and distally directed NF whilst the second through fifth had primarily secondary-sized and proximally directed NF. The topographical anatomy of the metatarsal diaphyseal NF appears similar across the South African populations. Metatarsal bones are highly vascularized bones presenting with multiple nutrient foramina.