Lipid peroxidation traditionally has been regarded as the major process causing damage to the brain by oxygen radicals and, subsequently, some forms of age-related deterioration. The brain, with its high oxygen consumption and abundance of polyunsaturated fatty acids, is at risk for oxidative damage. Although a great number of reports have associated lipid peroxidation with neurodegenerative diseases, the precise target of lipid peroxidation remains unclear. The aim of this study was to clarify the precise target of lipid hydroperoxides in neuronal cells. In this study, we showed the deleterious effect of phosphatidylcholine hydroperoxides (PCOOHs) on PC12 cells before and after differentiation into neuronal cells. Cell viability was significantly decreased in differentiated cells treated with PCOOH compared to undifferentiated cells treated in a similar way. PCOOH disrupted the formation of neurites and neuronal microtubules, which consist mainly of tubulin. Our results showed that differentiated cells were more vulnerable than undifferentiated cells to PCOOH and that PCOOH could attack microtubule-tubulin systems. This is the first study to clarify the neuronal loss of PC12 cells in the presence of PCOOH produced in early stages of neurodegenerative disease.