The application of fluorescent carbon nanodots (C-dots or CD), non-toxic particulate organic labels, to disease biomarker detection is still in its earliest stage of development. In the effort described here, a novel ratiometric immunoassay was developed to target a model protein disease biomarker, alpha-fetoprotein (AFP), using C-dot doped silica nanoparticles (CD-SNPs) and fluorescein isothiocyanate (FITC) as signaling agents. Highly fluorescent C-dots were hydrothermally synthesized from citric acid and ethylene diamine. The C-dots were then encapsulated in silicate shells to yield 45 nm nanoparticles using a novel reverse microemulsion method, enabling convenient handling (centrifugation and washing) and straightforward surface chemistry modification to facilitate development of bioassays. Capture antibody capped CD-SNPs (Ab1-CD-SNPs), together with FITC labeled antibodies (Ab2-FITC) constituted a new ratiometric immunosensor for AFP, in which CD-SNPs functioned as both solid supports for washing and separation and as built-in reference signaling agents to correct for inconsistent environmental effects. A calibration curve was established between the ratiometric signal (the ratio of fluorescence signals of FITC and C-dots, F/C) and AFP concentration in the broad range of 0.317-280 μg/dL, exhibiting a useful linear range (0.317-35 μg/dL, R 2 =0.9977), low detection limit (0.317 μg/dL) and acceptable recovery (105-120%). This assay format can be applied to a wide range of immunoassay targets. Our demonstration of encapsulating low-cost, easily synthesized, highly-fluorescent C-dots into silica nanoparticles for use in immunoassays will be useful in expanding future applications of these carbon nanomaterials to areas such as in-vivo cellular imaging, drug delivery, and in-vitro cell labeling and biomolecule sensing.