INTRODUCTION: Accurate complete blood count (CBC) reference intervals are essential for neonatal care. However, existing reference intervals do not account for key clinical variables such as sex, postnatal age, gestational age at birth and corticosteroid exposure. This study aims to establish updated CBC reference intervals for neonates admitted to a Neonatal Intensive Care Unit (NICU) while evaluating the effects of these factors on the CBC. METHODS: In this retrospective cohort study, all neonates admitted to the NICU at the John Radcliffe Hospital (Oxford, United Kingdom) between January 2022 and January 2023 were eligible for inclusion. Routine CBCs were included if there was no suspicion of infection or necrotising enterocolitis, no recent surgical interventions and no signs of clinical deterioration. The effects of sex, gestational age at birth and postnatal age were assessed for 48 parameters of the CBC using multivariate ANOVAs. Reference intervals were calculated at the 95% level. RESULTS: Among 3490 CBC results from 587 neonates, 386 results from 196 neonates met inclusion criteria. Sex-related differences were observed in nine parameters. Gestational and postnatal age both significantly influenced 34 parameters. Reference intervals were produced for all 48 CBC parameters, with histograms and boxplots illustrating variations by sex, postnatal age and gestational age. Secondary analyses highlighted the effects of corticosteroid exposure. CONCLUSIONS: We present reference intervals for 48 neonatal CBC parameters, highlighting the influence of sex, postnatal age, gestational age at birth and corticosteroid exposure. These findings improve the interpretation of neonatal CBCs and propose criteria for defining a sufficiently healthy neonatal population for diagnostic research.