The applications of in vivo bioluminescent imaging (BLI) with a luciferase reporter gene occur widely across biomedical fields. Luciferase-transgenic mice are highly useful donors for tracking transplanted ovarian tissues. Realizing the full potential of this system may greatly benefit the study of the physiological behaviour and function of transplanted grafts, and the rapid and reliable evaluation of new transplantation protocols. The ovarian tissues of donor FVB/N-Tg(PolII-Luc)Ltc transgenic mice, with a luciferase transgene as the reporter, were transplanted into iso/allogeneic recipients. Rejection, ovarian function and BLI were quantitatively analysed in vivo over time. The BLI of the ovarian isografts revealed longer survival than that of allografts, even with cyclosporine A (CsA) treatment. The CD4(+)/CD8(+) ratios of peripheral T-cells were significantly reduced in allografts compared with those in isografts (P<0.0001) during rejection, whereas CD19(+) cell numbers were higher in allografts. The infiltration of CD4(+)/CD8(+) cells into the graft was unremarkable in isografts from day 1, but was strong in allografts from day 8 onwards. Hormone activity revealed complete oestrus cycles in the isografts but only the dioestrus stage in the allografts. These results demonstrate that BLI in vivo expedites the fast throughput and fate maps of ovarian grafts. The use of BLI to longitudinally monitor ovarian grafts for immunorejection demonstrated the short survival of allografts and the much longer survival of isografts. CsA treatment alone is ineffective against the acute rejection of ovarian allografts.