Bone marrow stem cells (BMSCs) are able to confer beneficial effects after transplantation into animals with ischemic brain injuries. This effect is probably mainly caused by the release of trophic factors, though the possibility of dead neural cells being replaced by BMSCs cannot be excluded. The aim of this study was to determine whether the neuroprotective effects in question are dependent on direct cell-cell contacts between BMSCs and injured tissue. We therefore investigated that interplay in an in vitro model of hippocampal organotypic slice cultures (OHCs), in order to avoid the interference due to immunological rejection processes following transplantation in vivo. To perform ischemic injury in vitro, OHCs were made subject to oxygen-glucose deprivation (OGD). The possible direct or indirect neuroprotective effects induced by BMSCs were evaluated 24 h after injury by reference to two experimental paradigms using ischemic injured hippocampal slices: (i) cell transplantation on the top of OGD-treated OHC, (ii) co-cultivation of cell culture with OHC space separated for 24 h. In both paradigms, the BMSC treatment induced comparable and significant neuroprotection in OGD-injured OHCs. This effect increased after treatment with serum-deprived BMSCs, enriched with cells expressing nestin and GFAP. Comparing cell transplantation and cell co-cultivation with injured tissue, we concluded that the neuroprotective effect of BMSCs evoked shortly after ischemia (24 h) does not depend on cell-cell contacts. Additionally OGD-treated OHC was found to stimulate co-cultured BMSCs into expressing higher levels of bFGF and NGF. Finally, ischemic hippocampal slices increased the expression of nestin and GFAP in co-cultivated BMSCs, as well as changing their morphology.