Drosophila melanogaster is emerging as an important model system for neurodegenerative disease research. In this protocol, we describe an efficient method for imaging amyloid deposits in the Drosophila brain, by the use of a luminescent-conjugated oligothiophene (LCO), p-FTAA polymer probe. We also demonstrate the feasibility of co-staining with antibodies and compare the LCO staining with standard amyloid-specific probes. The LCO protocol enables high-resolution imaging of several different protein aggregates, such as Abeta1-42, Abeta1-42(E22G), Transthyretin V30M and human Tau, in the Drosophila brain. Abeta and Tau aggregates could also be distinguished from each other because of distinct LCO emission spectra. Furthermore, this protocol enables three-dimensional brain mapping of amyloid distribution in whole-mount Drosophila brains. The use of p-FTAA combined with other probes, antibodies and/or dyes will aid the rapid characterization of various amyloid deposits in the rapidly growing number of Drosophila models of neurodegenerative diseases.