A series of boron-functionalized BODIPY dyes with cyano groups were prepared from their corresponding BF2derivatives using SnCl4/TMSCN at room temperature for 10 min. Replacement of the fluorines by cyano groups reduces the B–N bond lengths, decreases the charge on boron, and causes characteristic [Formula: see text]B NMR chemical shifts. The 4,4[Formula: see text]-dicyano-BODIPYs show significantly enhanced stability to acidic conditions (excess TFA) and, with one exception, enhanced fluorescence quantum yields. Furthermore, the B(CN)2-BODIPYs were non-cytotoxic to HEp2 cells, both in the dark and upon exposure to light (1.5 J/cm[Formula: see text], and rapidly accumulated within cells, localizing mainly in the lysosomes, ER and Golgi.