Introduction: Biomarkers that will reliably predict the onset of Alzheimer's disease (AD) are urgently needed. Although cerebrospinal fluid (CSF) amyloid beta 1-42 (A beta 42), total tau, and phosphorylated tau can be used to complement the clinical diagnosis of AD, amnestic mild cognitive impairment (aMCI), the prodromal phase of AD, is heterogeneous. Biomarkers should be able to determine which patients with aMCI are at greatest risk of AD. Histological studies and animal models indicate that amyloid beta 1-43 (A beta 43) aggregates early, and may play a role in the pathological process of AD. We have examined levels of CSF A beta 43 in a 2-year longitudinal study of aMCI and early AD. Materials and Methods: Cerebrospinal fluid was collected at baseline, and after one and 2 years from patients with AD (n = 19), and patients with aMCI (n = 42). Of these, 21 progressed to AD during the 2 years of study, whereas 21 did not. Controls (n = 32) were lumbar punctured at baseline only. CSF analyses of A beta 43, A beta 42, and total tau were carried out with ELISA. Results: At baseline, CSF A beta 43, CSF A beta 42 and ratios with total tau could be used to separate controls from all three patient groups. CSF A beta 43, but not A beta 42, could separate patients with aMCI who progressed to AD during the 2 years of follow-up, from those that did not. The CSF total tau/A beta 43 ratio had a slightly but significantly larger area under the receiver operating characteristic curve when compared to the CSF total tau/A beta 42 ratio. CSF A beta 43 levels, but not A beta 42 levels, decreased from baseline to 2 years in the AD group. Discussion and Conclusion: CSF A beta 43 was demonstrated to be significantly reduced in patients already by the time that aMCI or AD was diagnosed, compared to controls, and this change must have occurred during the preclinical period. Since our results suggested that CSF A beta 43 distinguishes between subgroups of patients with aMCI better than CSF A beta 42, it may prove to be a useful additional biomarker for identifying aMCI patients at greatest risk of AD.