Eleven experimental immunofluorometric assays (IFMAs) were made using antibodies previously tested for epitope specificities. These assays were compared with six commercially available immunoassays. The clinical performance of these experimental assays was evaluated by analysing sera from 138 breast cancer patients and 105 female blood donors. The clinical performance of these assays was evaluated at a set specificity of 0.94. The highest overall sensitivity (0.56) was observed in the experimental assay with the antibody BC2 as solid phase and GP1.4 as the tracer antibody. This combination also showed the highest sensitivity in stage I/II breast cancer. The Truquant assay (Biomira) had an overall sensitivity of 0.51, and the highest sensitivity in stages III and IV at 0.65 and 0.94, respectively. The remaining commercial assays, with sensitivity ranging from 0.67 to 0.79, were below the top five experimental assays that showed sensitivity values between 0.79 and 0.85. The findings from our current study suggest that further development in MUC1 immunoassays could improve the detection of relapse in breast cancer patients.