Staining multiple samples for data acquisition with a flow cytometer is done in 96‐well plates to save time and make large data assessment in one working day possible. However, the inability of the FACScanⓇ to take up the samples from 96‐well plates is a major drawback. In order to avoid the individual transfer of samples to tubes, we have developed a system, which allows using the FACScanⓇ with 96‐well plates. The machine consists of a programmable control module and a loader which moves the 96‐well plate in 3 axis well by well along the sample collector. The machine is equipped with a wash buffer tank to avoid cross contamination of samples and a shaking option to avoid sedimentation of cells during acquisition. The machine can be further developed into a full automatic loader if connected to the FACS Station. In 24 hours about 7,000 samples with 10,000 cells each can be acquired.