Background Anaemia is a common presenting feature among patients with chronic kidney disease (CKD) and it is associated with poor clinical outcomes and quality of life. It is not clear if growth differentiation factor-15 (GDF-15) or hepcidin are useful as early markers of iron deficiency anaemia (IDA) among non-dialysis CKD patients. We therefore evaluated the diagnostic validity of GDF-15 and hepcidin as biomarkers of IDA among non-dialysis CKD patients in Johannesburg, South Africa. Method An analytic cross-sectional study was conducted among non-dialysis CKD patients (n=312) and apparently healthy controls (n=184) from June to December 2016 at an Academic Hospital, in Johannesburg, South Africa. An interviewer administered proforma was used to obtain the Socio-biological and clinical characteristics of the participants. Serum levels of GDF-15 and hepcidin were determined Predictive logistic regression models were built and post estimation receiver operator characteristics was determined to evaluate diagnostic validity of hepcidin and GDF-15 for absolute and functional iron deficiency anaemia. Results About half (50.6%) of the participants were female while the participants’ mean age was 49.7 ±15.8 years. The predictive value of diagnosing absolute IDA among CKD patients using GDF-15 was 74.02% (95% CI: 67.62% - 80.42%) while the predictive value of diagnosing functional IDA among CKD patients using hepcidin was 70.1% (95% CI: 62.79% - 77.49%).There was a weak negative correlation between hepcidin levels and GFR (r=-0.19, p=0.04) in anaemic CKD patients, and between serum GDF-15 and haemoglobin (r=-0.34, p=0.001). Serum ferritin (β=0.00389, P-value<0.001), was a predictor of log hepcidin. MCHC (β= -0.0220, P-value 0.005) and CKD stage (β=0.4761, P-value <0.001), race (β = 0.3429, P-value = 0.018) were predictors of log GDF-15. Both GDF-15 (adj OR: 1.0003, 95%CI: 1.0001 – 1.0005, P=0.017) and hepcidin (adj OR: 1.003, 95%CI: 1.0004 – 1.0055, P=0.023) were associated with iron deficiency anaemia after multiple linear regression modelling.Conclusion Serum GDF-15 is a potential biomarker of absolute IDA, while hepcidin levels can predict functional IDA among CKD patients.