Background Little is known about the genetic factors and downstream molecular pathways determining individual variability in fluid and imaging biomarkers associated with Alzheimer’s disease(AD). We studied polygenic risk scores (PRS) and pathway‐specific PRS in relationship with AD fluid and imaging biomarkers, in non‐demented individuals from the European Prevention of Alzheimer’s Dementia (EPAD) cohort. Method EPAD inclusion criteria were age>50 and Clinical Dementia Rating≤0.5 (n = 1886, Table 1). AD‐PRS was based on 85 previously identified loci, including and excluding APOE (PRSAPOE, PRSnoAPOE)1. Using gene‐variant and variant‐pathway mapping2, six pathway‐specific PRSnoAPOE were identified:1) immune‐activation, 2) signal‐transduction, 3) inflammatory‐response, 4) migration, 5) amyloid‐production, and 6) clearance. Linear models were used to assess the relationship of all PRS with fluid AD biomarkers, including Aβ1‐42, p‐Tau181, and t‐tau; and several imaging biomarkers, including hippocampal volume, global and lobar white matter hyperintensities (WMH) volumes, fractional anisotropy (FA) in 14 regions of interest from diffusion tensor imaging, and 10 resting‐state network connectivity from functional MRI. Models were adjusted for age, sex, site, and multiple comparisons. Result Models’ coefficients are reported in Table 2. PRSAPOE was significantly associated with decreased Aβ1‐42, and increased p‐Tau181 and t‐Tau. PRSnoAPOE showed a weaker, but still significant, negative association with Aβ1‐42 levels, and a significant positive association with p‐Tau181 and t‐Tau. Aβ1‐42 was only significantly associated with the migration, amyloid, and clearance pathways, while all pathways were significantly positively associated with p‐Tau181 and t‐Tau. Hippocampal volume was only significantly associated with PRSAPOE. Regarding WMH load, PRSAPOE showed a positive association with global, frontal periventricular, and parietal deep lobes. Furthermore, the clearance pathway was related to WMH load in all regions, most strongly in periventricular areas. Only the migration pathway was related to increases in FA in the splenium, body, and genu of the corpus callosum. Only the PRSAPOE was related to reduced functional connectivity (FC) in the default mode, control, and visual networks. Conclusion We show that genetic risk beyond APOE facilitates the manifestation of AD related pathologies. Moreover, clearance and migration pathways were associated with neuroimaging measures of white matter integrity, while FC and hippocampal volume were associated with overall AD genetic risk.