Fluorescent nanoparticle (NP) labels are of great interest for point-of-care medical diagnostics where high fluorescence signals combined with low limits of detection are required. In this work, hydrophilic and hydrophobic fluorescein dye derivatives were covalently doped into silica NPs. The NPs were prepared in a range of sizes from 16 to 80 nm using both ternary and quaternary microemulsion methods where the diameter varied linearly with changes in the water to surfactant ratio. The morphology and colloidal stability of the NPs were characterised using transmission electron microscopy and photon correlation spectroscopy; NPs doped with hydrophobic fluorescein dye were significantly smaller and more polydispersed. Optical properties including absorption, fluorescence and quantum efficiency were also determined. Representative NPs from each microemulsion method (ternary, Ø = 25 nm and quaternary, Ø = 80 nm) were tested as labels in a fluorescence based immunoassay for the detection of human IgG and human chorionic gonadotropin. Both sets of nanoparticle assays showed lower limits of detection and better coefficients of variance than a free dye label with good day to day reproducibility. The optimal surface coverage of detection antibody was also found to depend on the size of the nanoparticle.