Results analyzing the association between polymorphisms in the promoter region of the apolipoprotein E (APOE) gene and Alzheimer's disease (AD) are contradictory. We studied the association of three polymorphisms in the APOE promoter (-219T/G, -491A/T and -427T/C) with AD in a sample of the Colombian population. The polymorphism -491A/T confers increased risk for AD associated with AA genotype independent of APOEe4 allele (odds ratio (OR): 2.64) and more pronounced in men (OR: 6.07). Genotypes TT and TG of -219T/G showed a significant association with AD, but this was lost in an adjusted model. We did not find any association with -427T/C polymorphism. Using a haplogroup analysis of the promoter polymorphisms, we further confirmed their independent contribution as genetic risk factors for AD.