Background Asphyxia neonatorum may result in multiorgan dysfunction including renal involvement. There is no consensus on the determination of acute kidney injury (AKI) in neonates making establishment of the diagnosis and its management becomes difficult. The Acute Kidney Injury Network (AKIN) recommends AKI criteria based on increased serum creatinine level and reduced urine output. Objectives To identify the prevalence of AKI in asphyxiated neonates using the AKIN criteria, to compare the difference of AKI stages, and the glomerular filtration rates (GFR) between moderate and severe asphyxia. Methods This was a cross-sectional analytical study conducted between July 2012 and January 2013. Subjects were all asphyxiated neonates (Apgar score < 7 at fifth minute) with gestational age of >35 weeks delivered and hospitalized in Cipto Mangunkusumo Hospital and Koja District Hospital, Jakarta, Indonesia. Glomerular filtration rate was calculated using the components of urine creatinine, serum creatinine, and urine output; while AKI stages were determined according to AKIN criteria. Urinary output was measured via urethral catheterization. Results Of 94 subjects, there were 70 neonates with moderate and 24 neonates with severe asphyxia, with the prevalence of AKI was 63%. Twenty one out of 24 neonates with severe asphyxia experienced AKI, while neonates with moderate asphyxia who experienced AKI was 38 out of 70 subjects (54%). Two third of neonates with severe asphyxia who experienced AKI had stage 3 of AKI. More severe AKI stages and lower median GFR were found in neonates with severe compared to moderate asphyxia (P<0.001) . Conclusion The prevalence of AKI in neonatal asphyxia is high (63%). The more severe degree of neonatal asphyxia, the more severe AKI stage and the lower median GFR.