The synthesis, optical properties, and cellular uptake of a family of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) derivatives that incorporate a naphthyridine substituent at the 8-position of the BODIPY core and either alkyl, bromo, or dimethylamino aryl groups at the 2- and 6-positions are described. The family of compounds is classified, based on their optical properties, into two types; ClassI, compounds with alkyl substituents at the 2- and 6-positions show intense solvent-independent emission, which arises from the BODIPY core with no involvement of the naphthyridine. ClassII, the dimethylaminoaryl-containing compounds exhibit charge transfer transitions that lead to NIR fluorescence and remarkably large Stokes shifts, which make them potentially attractive in bioimaging. ClassII compounds exhibit complex solvent dependence. There is evidence for dual fluorescence from multiple rotamers; this is rationalized with the aid of time-dependant density functional theory (TDDFT) calculations. A representative compound from each class was PEGylated, which rendered them water soluble, but their photophysical properties were maintained in aqueous buffered media. The uptake of the PEGylated BODIPY compounds and the nonPEGylated parent compounds by live mammalian cells was compared by using confocal fluorescence microscopy and resazurin blue cytotoxicity assays were performed. All compounds tested exhibited good cell uptake, were largely nuclear excluding, and had low toxicity at 10μM. This is to our knowledge the first demonstration of such a mega-Stokes-shifted BODIPY probe in cell imaging. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.