Background: Lipidomic studies related to Alzheimer’s disease have been reported on either biological fluids or large human brain samples. For a better understanding of the role of lipids, especially during the amyloid-β peptide aggregation, it is crucial to determine the composition of the senile plaque versus the surrounding tissue, that is, the neuropil. Results: A laser microdissection step was added to the analysis by UPLC–MS/MS. Despite the very low amount of sample, two phosphatidylcholines that were significantly depleted in the senile plaque were identified. Conclusion: Changes in the phospholipid content have been shown between senile plaque versus neuropil. Nano HPLC, allowing a complete lipidomic profile, should further improve the results.