Europium-doped calcium hydroxyapatite and fluoroapatite nanophosphors functionalized with poly(acrylic acid) (PAA) have been synthesized through a one-pot microwave-assisted hydrothermal method from aqueous basic solutions containing calcium nitrate, sodium phosphate monobasic, and PAA, as well as sodium fluoride in the case of the fluoroapatite particles. In both cases a spindlelike morphology was obtained, resulting from an aggregation process of smaller subunits which also gave rise to high specific surface area. The size of the nanospindles was 191 (32) × 40 (5) nm for calcium hydroxyapatite and 152 (24) × 38 (6) nm for calcium fluoroapatite. The luminescent nanoparticles showed the typical red luminescence of Eu(3+), which was more efficient for the fluoroapatite particles than for the hydroxyapatite. This is attributed to the presence of OH(-) quenchers in the latter. The nanophosphors showed negligible toxicity for Vero cells. Both PAA-functionalized nanophosphors showed a very high (up to at least 1 week) colloidal stability in 2-(N-morpholino)ethanesulfonic acid (MES) at pH 6.5, which is a commonly used buffer for physiological pH. All these features make both kinds of apatite-based nanoparticles promising tools for biomedical applications, such as luminescent biolabels and tracking devices in drug delivery systems.