Amyloid plaques made of aggregated Aβ amyloid peptide are a pathological hallmark in brains affected by Alzheimer's disease (AD). Moreover, the amyloid peptide may play a major role in the onset and development of the disease in association to other factors such as oxidative stress. Although the molecular nature of the amyloid toxic species is still unknown, there is experimental evidence pointing to their nonfibrillar nature. In the present paper, we report the use of synchrotron Fourier transform infrared microspectroscopy (μFTIR) for the study of the effect of two different types of Alzheimer's Aβ(1-40) aggregates (amyloid fibrils and granular nonfibrillar aggregates) on PC12 cultured cells. The principal component analysis (PCA) of the infrared spectra has been complemented with a correlation analysis, which permits one to study different spectroscopic parameters as a function of peptide aggregation. The results show that the treatment of PC12 cells with amorphous aggregates generates a higher degree of oxidation in the vicinity of the amyloid aggregates than the treatment with preformed amyloid fibrils. These results, which permit, for the first time, the in situ colocalization of amyloid aggregates and oxidized macromolecules in cell culture, are in agreement with previous data from our group, showing that oxidation was higher in regions surrounding amyloid plaques in human brain samples affected by AD.