Recently, biodegradable nanoparticles received increasing attention for pharmaceutical applications as well as applications in the food industry. With the current investigation we demonstrate chip electrophoresis of fluorescently (FL) labeled gelatin nanoparticles (gelatin NPs) on a commercially available instrument. FL labeling included a step for the removal of low molecular mass material (especially excess dye molecules). Nevertheless, for the investigated gelatin NP preparation two analyte peaks, one very homogeneous with an electrophoretic net mobility of mu = -24.6 +/- 0.3 x 10(-9) m(2)/Vs at the peak apex (n = 17) and another more heterogeneous peak with mu between approximately -27.2 +/- 0.2 x 10(-9) m(2)/Vs and -36.6 +/- 0.2 x 10(-9) m(2)/Vs at the peak beginning and end point (n = 11, respectively) were recorded. Filtration allowed enrichment of particles in the size range of approximately 35 nm (pore size employed for concentration of gelatin NPs) to 200 nm (pore size employed during FL labeling). This corresponded to the very homogeneous peak linking it to gelatin NPs, whereas the more heterogeneous peak probably corresponds to gelatin not cross-linked to such a high degree (NP building blocks). Several further gelatin NP preparations were analyzed according to the same protocol yielding peaks with electrophoretic netmobilities between -23.3 +/- 0.3 x 10(-9) m(2)/Vs and -28.9 +/- 0.2 x 10(-9) m(2)/Vs at peak apexes (n = 15 and 6). Chip electrophoresis allows analyte separation in less than two minutes (including electrophoretic sample injection). Together with the high sensitivity of the FL detection - the LOD as derived for the first main peak of the applied dye from the threefold standard deviation of the background noise values 80 pM for determined separation conditions - this leads to a very promising high throughput separation technique especially for the analysis of bionanoparticles. For gelatin NP preparations, chip electrophoresis allows for example the comparison of preparation batches concerning the amount of NPs and gelatin building blocks as well as the indirect assessment of the degree of gelatin cross-linking (from obtained FL signals).