The ATP-binding cassette, sub-family A, member 1 gene (ABCA1) is a candidate risk gene for late onset Alzheimer's disease (LOAD) as a consequence of its role in cholesterol transport and metabolism, which is implicated in LOAD risk. ABCA1 has been shown in mouse models to enable the clearance of amyloid-β peptide from the brain, through its role in the lipidation of apolipoprotein (APOE). Although recent large scale genome wide association studies (GWAS) have failed to find significant associations with common genetic variants in this gene and LOAD, rare variants in ABCA1 have been shown to influence plasma high-density lipoprotein cholesterol levels. Using next generation sequencing of pooled DNA samples, we sequenced all the coding regions of ABCA1 in 311 LOAD cases and 360 control individuals drawn from the Greek population to identify low frequency non-synonymous variation. There were a significantly higher proportion of rare non-synonymous variants in control individuals compared to AD cases, suggestive of a protective effect. These findings provide new evidence of an effect of ABCA1 variants on AD risk. In addition they highlight the importance of high throughput sequencing in the identification of rare variation undetected by GWAS, but with the potential to have a strong effect on risk of LOAD.