Background: Non-esterified fatty acid (NEFA) levels are an important diagnostic tool in the investigation of neonatal hypoglycaemia. NEFA reference intervals have not been reported for neonates previously. Methods: The objective of this study was to determine an NEFA reference interval for neonates. Results: Heparinized plasma obtained from 106 healthy neonates in the first week of life was analysed using the Roche "Free fatty acid, Half-micro test" kit. Results were then analysed statistically for normality (Shapiro-Wilk test) and reference interval determined non-parametrically (bootstrap method). Conclusions: NEFA levels displayed a non-Gaussian distribution and the reference interval (2.5th and 97.5th percentiles) was 0.2-1.5 mmol/L (90% confidence intervals 0.1 -0.3 and 1.4-2.0 mmol/L, respectively). The NEFA reference interval in South African neonates less than a week old is similar to that described in infants (1-12 months), indicating that this reference range can be used over the entire neonatal period.