The objective of this study was to establish the interobserver reliability for superior mesenteric artery (SMA) and renal artery (RA) Doppler blood flow velocity (BFV) measurements in neonates. Forty-two clinically stable infants were enrolled, mean (SD) gestational age 33 (2) weeks, birthweight 2.00 (0.54) kg, postnatal age 10 (11) days. Doppler recordings were made by two trained observers. The SMA and RA were studied with a 5.0-MHz phased array transducer. The optimal spectral trace from each artery containing a minimum of five consecutive waveforms was analysed. The peak systolic velocity (PS), end diastolic velocity (ED) and mean peak velocity (MV) were measured and the time-averaged mean velocity (TAV) and waveform indices were calculated. Using the intraclass correlation coefficient (ICC) the estimates of interobserver reliability for different measurements varied from 0.40 to 0.83. Substantial agreement was obtained between observers in the TAV, PS, ED and MV; the ICC varied from 0.72 to 0.83 demonstrating that Doppler BFV measurements of the SMA and RA are reliable in neonates.