INTRODUCTION: Whole genome methylation sequencing (WGMS) in blood identifies differential DNA methylation in persons with late-onset dementia due to Alzheimer's disease (AD) but has not been tested in persons with mild cognitive impairment (MCI). METHODS: We used WGMS to compare DNA methylation levels at 25,244,219 CpG loci in 382 blood samples from 99 persons with MCI, 109 with AD, and 174 who are cognitively unimpaired (CU). RESULTS: WGMS identified 9756 differentially methylated positions (DMPs) in persons with MCI, including 1743 differentially methylated genes encoding proteins in biological pathways related to synapse organization, dendrite development, and ion transport. A total of 447 DMPs exhibit progressively increasing or decreasing DNA methylation levels among CU, MCI, and AD that correspond to cognitive status. DISCUSSION: WGMS identifies DMPs in known and newly detected genes in blood from persons with MCI and AD that support blood DNA methylation levels can distinguish cognitive status. HIGHLIGHTS: Whole genome methylation levels in blood from 99 persons with mild cognitive impairment (MCI), 109 with Alzheimer's disease, and 174 who are cognitively unimpaired were analyzed. Nine thousand seven hundred fifty-six differentially methylated positions (DMPs) were identified in MCI. One thousand seven hundred forty-three genes comprise one or more DMPs in persons with MCI. Fifty-eight DMPs and 392 differentially methylated genes are shared among the three pairwise comparisons. Four hundred forty-seven DMPs exhibit progressive changes that correspond to cognitive status.