The risk of acute kidney injury (AKI) in hospitalized critically ill neonatal populations without primary renal disease continues to be high, in both term and premature infants. Observational studies have revealed high rates of chronic kidney disease (CKD) in survivors of neonatal AKI. Proposed mechanisms underlying the progression of CKD following AKI include nephron loss and hyperfiltration, vascular insufficiency and maladaptive repair mechanisms. Other factors, including prematurity and low birth weight, have an independent relationship with the development of CKD, but they may also be positive effect modifiers in the relationship of AKI and CKD. The large degree of heterogeneity in the literature on AKI in the neonatal population, including the use of various AKI definitions and CKD outcomes, has hampered the medical community’s ability to properly assess the relationship of AKI and CKD in this vulnerable population. Larger prospective cohort studies with control groups which utilize recently proposed neonatal AKI definitions and standardized CKD definitions are much needed to properly quantify the risk of CKD following an episode of AKI. Until there is further evidence to guide us, we recommend that all neonates with an identified episode of AKI should have an appropriate longitudinal follow-up in order to identify CKD at its earliest stages.