Background: Evaluation of metabolites that are directly involved in the physiological process, few steps short of phenotypical manifestation, remains vital at unraveling the biological moieties involved in the development of the (MDD) and in predicting its treatment outcome. Methodology: Eight bio-fluids ( 8 urine and 8 serum samples) obtained from consenting healthy controls (HC), twenty five (25) biofluids from first episode treatment naïve MDD (TNMDD) patients and twenty (22) biofluids from treatment naïve MDD patients 2 weeks after SSRI treatment (TWMDD) were analysed for metabolites using proton nuclear magnetic resonance (1HNMR) spectroscopy. The evaluation of patients’ samples was carried out using Partial least squares discriminant analysis (PLSDA) and Orthogonal Partial Least Square-Discriminant Analysis (OPLSDA) models. Results: In the serum, decreased levels of lactate, glucose, glutamine, creatinine, acetate, valine, alanine, and fatty acid and an increased level of acetone and choline in TNMDD or major depressive disorder patients 2 weeks after SSRI treatment (TWMDD) irrespective of whether an OPLSDA or PLSDA evaluation was used were identified. A test for statistical validations of these models was successful. Conclusion: Only some changes in serum metabolites levels between HC and TNMDD identified in this study have potential values in the diagnosis of MDD. These changes included decreased levels of lactate, glutamine, creatinine, valine, alanine, and fatty acid as well as an increased level of acetone and choline in TNMDD. The diagnostic value of these changes in metabolites was maintained in samples from TWMDD patients, thus reaffirming the diagnostic nature of these metabolites for MDD.