Heterogeneous fluorescence immunoassays have been automated using flow injection manifolds incorporating thiophilic gel solid phase reactors to separate antibody-bound and unbound analyte molecules. Antibody elution is achieved by changes in ionic strength, thus allowing the use of pH sensitive fluorescent labels. This facilitates the development of dual analyte systems, in which two competitive immunoassays with separate labels are monitored in parallel. Detection of the fluorophores by high speed synchronous fluorescence scanning while the flow is briefly stopped utilises either one synchronous interval which detects both fluorophores, or two separate scans at different wavelength intervals, one for each fluorophore. Simultaneous analyses of serum albumin and transferrin exemplify these novel approaches. Spectroscopic interferences are very small, analyte recoveries are close to 100%, with a relative standard deviation of 5–6% and a sampling rate of 20 h⁻¹.