The current work explores the CSF of three groups of subjects: non-demented (ND) control group, MCI due to AD (which offers the opportunity to study the disease progression), and AD. Nontarget LC-HRMS was performed coupled to two different analytical columns and using various software and cheminformatics approaches for data analysis to detect small molecules potentially associated with disease progression, complemented by a highly sensitive target LC-MS method to quantify extremely low concentrations of BAs in CSF. Finally, the potential associations between clinical AD biomarkers (Aβ1-42, t-Tau, p-Tau and NfL) and chemicals identified in the CSF were investigated to determine which small molecule signatures could serve as potential biomarkers of disease progression for future investigations in a larger cohort of patients.