Magnetic microplate assemblies are disclosed for assaying of biological activated magnetic particles from a supernatant. The assemblies include a magnetic microplate holder and a microplate including a plurality of wells for retaining the magnetic particles. The microplate holder includes a plurality of magnets for attracting the magnetic particles to the wells and a plurality of detents for securing the microplate in the holder. The detents allow the microplate to be tightly retained in the holder when the assembly is turned over to discard supernatant and wash buffer applied to rinse supernatant from the magnetic particles.