This research paper addresses the hypothesis that the in vivo criterion of bovine somatic cell count (SCC) < 200,000 cells/ml milk as a diagnostic marker for healthy mammary tissue is not suitable to be adopted to milk samples taken post slaughter. To study immune mechanisms associated with intramammary infections, we developed a mammary explant model. As SCC is routinely applied to differentiate between healthy and inflamed mammary tissue, donor cows were selected based on their milk SCC obtained in vivo. Furthermore, milk cell differentiation for early mastitis detection via flow cytometry allows identification of leucocyte subpopulations and complements SCC. To replace in vivo examination and allow for post mortem selection of donor cows, this explorative study aimed to investigate how slaughter influences the reliability of SCC and differential milk cell count (DMCC) and to assess their validity as diagnostic markers for udder health in bovine milk samples obtained post slaughter. Therefore, quarter milk samples from cows were obtained in vivo and post mortem and analysed to determine SCC and DMCC and identify major mastitis pathogens. The logarithmized numbers of SCC, non-viable cells, viable cells, lymphoid cells, polymorphonuclear (PMN) and large cells per ml milk were compared using linear mixed-effects models in milk samples obtained from cows in vivo and post mortem. The number of lymphoid cells, PMN and large cells was significantly higher in milk samples obtained post mortem than in vivo, with PMN being the most prominent cell population. Higher milk SCC values measured post mortem might be explained by migration of leucocytes into the periphery during slaughter. This should be considered when modelling intramammary infection in vitro using udder tissue. Reflecting these findings, it is not feasible to endorse SCC as a reliable marker for post mortem selection of donor cows with healthy mammary tissue for in vitro models.