Abstract Flow cytometry (FC) allows for the quantification of individual cell populations whose levels are known to change in disease states, such as, the reduction in CD4+ T cells in AIDS. While FC is a powerful technique, it can be difficult to teach its principles and applications to undergraduate students. Assessing changes in cell populations is an excellent approach to teach FC, however obtaining real patient samples is not often possible. In addition, hands on use of a flow cytometer by students is difficult or impossible to achieve when class sizes are large. To address these challenges, we taught the principles of FC, sample preparation (Week 1) and data analysis (Week 2) of mock “control” and “patient” samples. In Week 1, the theory of FC was covered and the students labelled “control” and “patient” blood with anti-CD3, 4, 8, 14, 19 and 66 mAbs. In Wk 2, students were provided with data files where the levels of major cell populations had been manipulated using magnetic beads to mimic immune diseases states. Using written and video instructions for the software and supplied reference ranges, and using a PC, were asked to identify the disease status of their patient sample. Student perceived understanding of FC was found to significantly increase after the practical session, and student feedback was also overwhelmingly positive. The manipulation of cell populations in whole blood to mimic disease states is an excellent way to teach undergraduate students the major principles of FC. These include labelling of cells, learning to use the software, interpreting the data and disease diagnosis. We will continue to expand our list of disease conditions. All data files are freely available to any teaching staff who may wish to use them as part of their teaching.