The detection and localization of polymer-based nanoparticles in human bone marrow-derived stromal cells (hBMSC) by time-of-flight secondary ion mass spectrometry (ToF-SIMS) is reported as an example for the mass spectrometry imaging of organic nanoparticles in cell environments. Polyelectrolyte complex (PEC) nanoparticles (NP) made of polyethylenimine (PEI) and cellulose sulfate (CS), which were developed as potential drug carrier and coatings for implant materials, were chosen for the imaging experiments. To investigate whether the PEI/CS-NP were taken up by the hBMSC ToF-SIMS measurements on cross sections of the cells and depth profiling of whole, single cells were carried out. Since the mass spectra of the PEI/CS nanoparticles are close to the mass spectra of the cells principal component analysis (PCA) was performed to get specific masses of the PEI/CS-NP. Mass fragments originating from the NP compounds especially from cellulose sulfate could be used to unequivocally detect and image the PEI/CS-NP inside the hBMSC. The findings were confirmed by light and transmission electron microscopy. Graphical Abstract During ToF-SIMS analysis Bi3 (+) primary ions hit the sample surface and so called secondary ions (SI) are emitted and detected in the mass analyser. Exemplary mass images of cross sections of human mesenchymal stromal cells (red; m/z = 86.1 u) cultured with organic nanoparticles (green; m/z = 143.0 u) were obtained.