Synaptic pathology seems to be occurring early in Alzheimer's disease (AD) development and cognitive alterations in patients with AD are suggested to be associated with synaptic loss. The cerebrospinal fluid (CSF) biomarkers reflecting synaptic pathology might therefore be valuable for earlier diagnosis, assessment of progression of disease and evaluation of treatment. Synaptosomal-associated protein 25 (SNAP-25) is a component of the SNARE protein complex, that is involved in the regulation of the synaptic neurotransmitter release. We have developed a novel affinity mass spectrometry approach allowing reproducibly measurements of the low abundant proteolytic fragments of SNAP-25 in CSF samples from individual subjects. By applying this novel affinity mass spectrometry strategy on three separate cohorts of patients the SNAP-25 as a novel CSF biomarker for AD was assessed for the first time. The CSF SNAP-25 proteoforms were immunoprecipitated, digested with trypsin and stable isotope labeled peptides were added. Quantification of SNAP-25 was performed by high resolution selected ion monitoring (HR-SIM-MS) on a Quadrupole-Orbitrap Mass Spectrometer (Q Exactive). The first clinical set of CSF samples were from patients with prodromal AD (N=7), AD (N=9) and controls (N=9) (German cohort). The second clinical material consisted of CSF samples from non-demented controls (N=6) and patients with AD (N=10) (Swedish cohort I). The third clinical material consisted of CSF samples from healthy controls (N=16) and patients with AD (N=17) (Swedish cohort II). Levels of CSF SNAP-25 were found to be increased in early as well as later stages of AD in three independent case-control cohorts. Almost all of the measured tryptic peptides of SNAP-25 could differentiate AD from controls with an area under the curve of 0.800 to 1.000 depending on cohorts studied. We have developed a sensitive method to analyze SNAP-25 levels in individual CSF samples that to our knowledge never have been done before. Levels of CSF SNAP-25 were found to be increase in early as well as later stages of AD in three independent case-control cohorts suggesting SNAP-25 to be a valuable marker.