The present invention describes a global metabolomic profile of patients with community acquired pneumonia (CAP) and sepsis. The metabolomic profile of endogenous small molecules blood was determined using mass-spectrometry. The global metabolomic profile in plasma demonstrated broad differences between CAP and sepsis patients when comparing those who do and do not survive at 90 days. Increases in specific metabolite biomarkers displayed on a heat map provide early diagnosis of these medical conditions to allow for early intervention and aggressive treatment.