Nanoparticles have recently been demonstrated in a rat model to be a promising tool for targeting inflamed areas of the intestinal mucosa in inflammatory bowel diseases whilst concentrating anti-inflammatory drugs at their site of action. Still, however, this novel concept has to be proven in vivo in humans. As a first step biodegradable and biocompatible fluorescent nanoparticles were prepared and characterized to serve as markers for successful inflammation targeting in future clinical trials. To achieve stable fluorescence labelling, fluoresceinamine was covalently bound to poly(L-lactide-co-glycolide) (PLGA) as described by Horisawa et al. The modification rate of carboxyl-end groups of the PLGA chains determined by 1H NMR was 65%. From this modified polymer, nanoparticles (FA-PLGA nanoparticles) of approximately 270 nm size were prepared via nanoprecipitation. Apart from an initial burst effect, most of the label (> 88%) appeared to be strongly bound and was leaked only slowly from the particles. In contrast, we found an immediate leakage of encapsulated sodium fluorescein with nanoparticles prepared by a double emulsion method. In degradation experiments we studied and visualized the changes in morphology and elastic properties of the FA-PLGA nanoparticles within 15 weeks using atomic force microscopy. When FA-PLGA nanoparticles were applied on an in vitro model of the intestinal mucosa (Caco-2 cell culture), only minor amounts of their fluorescent degradation products (approximately 0.02% after 6 h) were transported. In a cytotoxicity study with Caco-2 cells, FA-PLGA nanoparticles yielded an IC50 value as for plain PLGA nanoparticles. In conclusion, the polymer modification method allows to prepare fluorescently labelled nanoparticles from a well-known biodegradable pharmaceutical polymer with sufficient stability to be monitored over a period of several days. Some initial leakage of fluorescence label appears to be unavoidable but negligible with respect to potential absorption and cytotoxicity when applied in vivo.