SummaryDuplex pulsed Doppler ultrasound was used to determine blood flow velocities in the coeliac axis and superior mesenteric artery in three groups of neonates: a group at high risk of developing necrotising enterocolitis (n = 27) and two control groups, i.e., a nonasphyxiated, appropriately grown group of preterm infants (n = 18) and a group of nonasphyxiated term infants (n = 14). Subjects were studied on the first, second, and fourth days of life. The median peak systolic velocities in the superior mesenteric artery were between 20 and 51% lower in the at‐risk group than in the term control group on all 3 days of measurement (p < 0.05 – p < 0.002). The ratio of peak systolic velocity in the coeliac axis to that in superior mesenteric artery, an index of relative downstream vascular resistance in the superior mesenteric artery, was 42–65% greater in the at‐risk group compared with the other two groups on days 1 and 2 (p < 0.05 – p < 0.001) and significantly greater than the term group on day 4 (73%, p < 0.002). These data demonstrate that neonates at risk of developing necrotising enterocolitis have abnormal gut blood flow velocities. Furthermore, they provide evidence that an alteration in the splanchnic circulation may be an important factor in the final common pathway that links diverse risk factors for necrotising enterocolitis with clinical disease.