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Background: The value of Cystatin C as a biomarker of Glomerular filtration rate (GFR) among African newborns is unknown, due to paucity of studies, restricting the measurement of GFR in this population of newborns to creatinine clearance despite its limitations. This study was therefore conducted to estimate GFR from serum Cystatin C in a population of Nigerian newborns and explored the relationship with anthropometrics. Methods: This was a cross-sectional, analytical study. A total of 60 healthy preterm and 30 healthy term babies were recruited at a tertiary hospital in North-central, Nigeria. Serum Cystatin C was determined using ELISA according to standard methods. Anthropometric measurements were done with standard methods. The GFR was estimated using Zappitelli's equation. Data were analyzed using SPSS Version 20, and p-value < 0.05 was considered significant. Results: Mean serum Cystatin C was 1.20 ± 0.33 (range 0.80–2.20) mg/L with comparable values in males and females (1.19 ± 0.35 vs 1.15 ± 0.31 mg/L, p = 0.481)). Mean serum Cystatin C among preterm babies were higher than term babies (1.31 ± 0.36 vs 1.01 ± 0.11 mg/L, p = < 0.001). Mean estimated GFR was 65.36 ± 16.9 ml/min/1.732 and was comparable in males and females (64.39 ± 17.95 vs 66.52 ± 15.76 ml/min/1.73 m2,p = 0.555). Estimated GFR was lower among preterm than term babies (60.10 ± 17.53 vs 75.89 ± 9.1 ml/min/1.73 m2, p = < 0.001). Serum cystatin C and estimated GFR moderately correlated with gestational age and anthropometrics (length, occipitofrontal circumference and weight). Conclusions: Serum cystatin C as a biomarker GFR among newborns is low compared with most studies done out of Africa. The serum cystatin C and estimated GFR correlated with the gestational age and anthropometric parameters. The findings relationship between the serum Cystatin C, estimated GFR and anthropometrics among the newborns suggested a need for more studies. [ABSTRACT FROM AUTHOR]