Apolipoprotein E (ApoE) phenotyping was determined in 42 subjects with Alzheimer’s disease (AD), 49 with depression, including 26 with early-onset depression (EOD) and 23 with late-onset depression (LOD), and 49 controls. In the EOD group, the frequency of the ApoE Ε4 allele was not different from the control frequency (p = 0.532) but was significantly lower than in AD (p < 0.001). In the LOD group, the ApoE Ε4 frequency was significantly higher than in the controls (p = 0.034) but was not different from that in the AD group (p = 0.229). Individuals with ApoE Ε4 were at greater risk of getting AD (odds ratio, OR = 5.5, 95% confidence interval, CI, 2.0–14.0) or LOD (OR = 6.1, 95% CI, 1.9–19.0) than of EOD (OR = 0.7, 95% CI, 0.2–2.5). These results suggest an association between the ApoE Ε4 allele frequency and LOD. Patients with LOD could be at risk of developing AD by an Ε4-dependent pathway.