<jats:title>Introduction</jats:title><jats:p>Late-onset Alzheimer’s disease (LOAD, onset age > 60 years) is the most prevalent dementia in the elderly<jats:sup>1</jats:sup>, and risk is partially driven by genetics<jats:sup>2</jats:sup>. Many of the loci responsible for this genetic risk were identified by genome-wide association studies (GWAS)<jats:sup>3–8</jats:sup>. To identify additional LOAD risk loci, the we performed the largest GWAS to date (89,769 individuals), analyzing both common and rare variants. We confirm 20 previous LOAD risk loci and identify four new genome-wide loci (<jats:italic>IQCK</jats:italic>, <jats:italic>ACE</jats:italic>, <jats:italic>ADAM10</jats:italic>, and <jats:italic>ADAMTS1</jats:italic>). Pathway analysis of these data implicates the immune system and lipid metabolism, and for the first time tau binding proteins and APP metabolism. These findings show that genetic variants affecting APP and Aβ processing are not only associated with early-onset autosomal dominant AD but also with LOAD. Analysis of AD risk genes and pathways show enrichment for rare variants (<jats:italic>P</jats:italic> = 1.32 × 10<jats:sup>−7</jats:sup>) indicating that additional rare variants remain to be identified.</jats:p>