A new fluorescent analytical methodology for the quantification of peroxynitrite (ONOO(-)) in the presence of nitric oxide (NO) was developed. The quantification of ONOO(-) is based in the oxidation of the non-fluorescent reduced fluoresceinamine to a high fluorescent oxidized fluoresceinamine in reaction conditions where the interference of NO is minimized. Screening factorial experimental designs and optimization Box-Behnken experimental design methodologies were used in order to optimize the detection of ONOO(-) in the presence of NO. The factors analysed were: reduced fluoresceinamine concentration (C( Fl)); cobalt chloride concentration (C(CoCl2)); presence of oxygen (O(2)); and, the pH (pH). The concentration of sodium hydroxide (C(NaOH)) needed to diluted the initially solution of ONOO(-) was also evaluated. An optimum region for ONOO(-) quantification where the influence of NO is minimal was identified - C(Fl) from 0.50 to 1.56 mM, C(CoCl2) from 0 to 1.252 × 10(-2) M, pH from 6 to 8 and C(NaOH) 0.10 M. Better results were found in the presence of NO at pH 7.4, C(Fl) 0.5 mM, without oxygen, without cobalt chloride and with a previous dilution of peroxynitrite solution with C(NaOH) 0.1 M. This methodology shows a linear range from 0.25 to 40 μM with a limit of detection of 0.08 μM. The bioanalytical methodology was successfully applied in the ONOO(-) quantification of fortified serum and macrophage samples.