AbstractFluorescent cell analytical techniques require the incorporation of a fluorophore into the target molecule without causing a significant change in the native conformation. Many short peptides have a limited number of reactive groups that can be labeled without affecting the biological activity. In this work we present several methods for labeling β‐amyloid peptides (βA[25–35], βA[1–40]) and their derivatives (LPFFD, RIIGL and RVVIA) with different chromophores exclusively at the N‐terminus. In the case of liquid‐phase labeling, fluorescein isothiocyanate was used. The side‐chain amino function of Lys, if present in the sequence, was protected with an Fmoc group, whereby the hydrophobic character of the peptide was further increased. The labeling reaction was carried out in an appropriate deaggregating solvent, DMSO. For solid‐phase labeling, 5(6)‐carboxyfluorescein and 7‐amino‐4‐methyl‐3‐coumarinylacetic acid were applied. Several cleavage cocktails were tested for removal of the labeled amyloid peptides from the resin in order to completely suppress the oxidation of Met. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.