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High Tc SQUID system is developed for the detection of the biological binding-reaction between antigen and its antibody. In this measurement, the antibody is labeled with magnetic nanoparticles, and the magnetic signal from the nanoparticles is measured. The excitation field of a few mT is applied in parallel to the SQUID in order to magnetize the nanoparticles. Due to mechanical misalignment, however, the vertical component of the excitation field couples to the SQUID, and degrades the system performance. In order to solve this problem, we develop two methods. One is the use of a compensation field in the case of the flux dam, and the other is the use of a switch instead of the flux dam. We also develop a magnetic marker utilizing Fe3O4 nanoparticle with diameter of d=25 nm. The nanoparticle is embedded in the polymer with typical diameter of 80 nm, and COOH is attached around the surface of the polymer. The properties of the marker are discussed.