Distinction between closely related and morphologically similar cells is difficult by conventional methods especially without labelling. Using nuclear targeted gold nanoparticles as intracellular probes we demonstrate the ability to distinguish between progenitor and differentiated cell types in a human neuroblastoma cell line using surface-enhanced Raman spectroscopy (SERS). SERS spectra from the whole cell area as well as only the nucleus were analysed using principal component analysis which allowed unambiguous distinction of the different cell types. SERS spectra from the nuclear region showed the developments during cellular differentiation by identifying an increase in DNA/RNA ratio and proteins transcribed. Our approach using nuclear targeted AuNPs and SERS imaging provides label-free and non-invasive characterization which can play a vital role in identifying cells types in bio-medical stem cell research.