Apolipoprotein E4 (apoE4) has been identified as a major risk factor for Alzheimer disease (AD). Previously it has been reported that levels of apoE are reduced in cerebrospinal fluid (CSF) of AD patients. Because it is known that apoE4 affects plasma lipid metabolism, we examined whether the presence of apoE4 might correlate with an altered lipid metabolism in the CSF of control subjects and AD patients. ApoE and lipid concentrations were determined in postmortem ventricular CSF of 30 neuropathologically confirmed AD cases and 31 age-matched control patients. ApoE genotyping was performed on frozen brain tissue of the same patients. In line with other reports, we found an increased APOE*4 allele frequency in the AD group (0.461) when compared with the control group (0.225). ApoE levels in CSF of AD patients were not significantly reduced when compared with the controls (mean ± SD: 63 ± 55 and 82 ± 62 μg/dL for AD and controls, respectively). However, in the CSF of AD patients levels of free and esterified cholesterol (0.13 ± 0.09 and 0.25 ± 0.19 mg/dL, and 0.25 ± 0.19 and 0.42 ± 0.34, respectively), phospholipids (0.2 ± 0.1 and 3.5 ± 5.0 mg/dL) and, suprisingly, also fatty acids (4.5 ± 3.2 and 28.0 ± 18.5 μmol/L) were found to be significantly reduced. After correction for age, sex, postmortem delay, and pH the levels of phospholipids, fatty acids, and free cholesterol were still significantly reduced (p = 0.021, p = 0.026, and p = 0.012, respectively). The apoE and lipid levels in CSF of AD-and control patients appeared not to be affected by the number of APOE*4 alleles. In conclusion, our results suggest an altered lipid homeostasis in the brain of AD patients that is not related to the presence of apoE4. It is, therefore, unlikely that an effect of apoE4 on brain lipid metabolism is the underlying mechanism behind the role of apoE4 in the development of AD.