Neonatal sepsis is a clinical syndrome characterized by symptoms and signs of infection in the first twenty-eight days of life. Serum thyroid, cortisol and hepcidin are affected by neonatal sepsis. ; Aim of the Work: The aim of this study was to assess the diagnostic value of serum thyroid hormones including free triiodothyronine (free TT3) and free tetraiodothyronine (free TT4), serum cortisol and hepcidin levels through comparison of their concentrations between normal neonates and neonates with high probable late-onset sepsis. ; Patients and Methods: This case-control study was carried out on 40 neonates with suspected high probable late-onset neonatal sepsis based on clinical and laboratory finding who were admitted to NICU of Pediatric Department, Tanta University, Egypt in the period from April 2017 to May 2019 (group I) and 40 healthy neonates matched in age and sex as a control group (group II). For patients and controls, blood culture, highly sensitive C-reactive protein (H-s CRP), serum hepcidin, serum cortisol and thyroid hormones levels including free TT3 and free TT4 were assessed. ; Results: There were no significant differences between studied groups regarding weight, gestational age, sex and mode of delivery. H-s CRP, serum cortisol and hepcidin were significantly higher in group I than group II while serum-free TT3 and free TT4 were significantly lower in group I compared with controls (group II). There was significantly lower H-s CRP, serum hepcidin and cortisol and significantly higher serum-free TT3 and free TT4 in group I after antibiotic therapy compared to the same group before treatment while there were no significant differences between group I after antibiotic therapy and control group (group II) regarding the same parameters. There was a significant positive correlation between H-s CRP and serum hepcidin and cortisol in group I while there was a significant negative correlation between H-s CRP and free TT3 and free TT4. ROC curve of specificity and sensitivity of H-s CRP, serum hepcidin, cortisol, free TT3 and free TT4 in the prediction of neonatal sepsis shows that serum hepcidin had the highest sensitivity and specificity with 95% and 90% respectively followed by serum cortisol, H-s CRP, free TT3 and lastly free TT4. ; Conclusion and Recommendations: Neonates with high probable sepsis had significantly higher serum cortisol and hepcidin and significantly lower free TT3 and free TT4 compared with healthy neonates. These findings may draw our attention about the use of these markers in the diagnosis of neonatal sepsis which can help in early treatment and subsequently better prognosis.