Fluorescent carbon nano-onions emitting in the far-red spectral window with enhanced solubility in biological media and bright photoluminescence are reported. , A new generation of fluorescent carbon nano-onions with enhanced solubility in biological media and bright photoluminescence is reported. The nano-onions functionalized with a water soluble boron dipyrromethene dye emit in the far red spectrum with a high quantum yield ( Φ F ) and are suitable for high resolution imaging. The nanoparticles are characterized by a variety of different analytical techniques such as thermogravimetric analysis, dynamic light scattering, zeta potential, electron microscopy, Raman, X-ray photoelectron and fluorescence spectroscopies. They are easily internalized by human breast cancer cells (MCF-7) without any significant toxic effects. Moreover, confocal imaging studies show they exhibit a high fluorescence intensity and are localized in the lysosomes at a very low concentration. Our findings confirm the excellent potentialities of these functionalized carbon nanomaterials as biocompatible platform for high resolution biological imaging.