Unique aspects of neonatal renal physiology enhance the occurrence of Acute Kidney Injury (AKI) as a complication of neonatal sepsis. The study sought to determine prevalence of AKI and its characteristics in neonates with suspected sepsis. A cross-sectional study was conducted at Kenyatta National Hospital among neonates aged 0-28 days. AKI was defined as serum creatinine of more than 100µmmol/l. Among 332 neonates included 120 had AKI giving a prevalence of 36.1% (95% CI 31 to 41.6). Based on RIFLE criteria the commonest AKI presentation was Failure 72 (62.6%, 95% CI 53.6 to 71.6), followed by Injury 26 (22.6%, 95% CI 14.8 to 30.4) and then Risk 17 (14.8%, 95% CI 8.2 to 21.3). AKI was more common in neonates with suspected late onset sepsis (p=0.004). Maternal fever in the preceding week to delivery and presence of either puerperal sepsis or post-partum hemorrhage were significantly associated with severe AKI (p=0.004 and p=0.038). Prevalence of AKI was high; those with suspected late onset sepsis were more likely to develop AKI compared to early onset sepsis. Presence of maternal fever preceding delivery and presence of either puerperal sepsis or postpartum hemorrhage were associated with severe forms of AKI.