Fluorescein isothiocyanate (FITC)-myoglobin conjugates were synthesized with a binding stoichiometry of one to three fluorophores per protein. FITC binding sites were determined by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). Five lysine residues and the N-terminal amino group were identified as preferential binding sites. The ground and excited-state absorption spectra and the fluorescence decay of the conjugates in the native and denatured state of the carrier protein were analyzed. For comparison, unbound FITC and FITC covalently bound to a polysaccharide (dextran) were studied. For FITC, FITC-dextran and the FITC-myoglobin conjugates, only one FITC absorption peak was obtained in the ground state spectrum. Similarly, the excited state absorption (ESA) spectra of unbound FITC and of FITC-dextran showed only one single maximum whereas two maxima were detected for the native FITC-myoglobin conjugates. One of these sub-bands disappeared following urea treatment of the conjugate. We conclude that ESA measurements of extrinsic fluorophores on proteins can be used to monitor different micro-environments of the fluorophore and to distinguish between different conformational states of the labeled protein. This method can be a useful tool for analysing coexisting protein conformations.