During folliculogenesis the granulosa cells differentiate into two cell types: Cumulus cells (CC) and mural granulosa cells (MGC). The objective of the study was to generate and compare the transcriptomes of MGC and CC from the pre-ovulatory follicle to characterize the detailed profile of the two cell populations shortly before ovulation.Twenty-one IVF/ICSI patients undergoing controlled ovarian stimulation (COS) donated CC and MGC from individual follicles containing metaphase-II oocytes. Cells were prepared immediately after recovery and mRNA was isolated for whole-genome-gene-expression analysis and RT-PCRs. Paired (within the individual follicle) comparisons between the CC and MGC expression profiles were performed and corrected for multiple comparisons.A total of 1562 genes were differentially expressed by >2-fold (p-value8-fold changed and represented specialised cellular functional categories such as inflammatory response, extracellular-matrix and cell-cell-communication while the 1406 genes 2-8-fold changed represented functional categories such as proliferation and lipid metabolism. Transcripts not previously linked to the follicle were found to be differentially expressed between CC and MGC suggesting specialized function in these compartments, e.g. pepsinogen-A was selectively expressed in MGC, while ryanodine-receptor-2 (RYR2) was selectively expressed in CC. Positive correlations were present between expression levels of RYR2 and the amphiregulin and gap-junction proteins.In conclusion, the transcriptomes of corresponding CC and MGC from individual pre-ovulatory follicles clearly revealed two distinct cell types. New as well as known genes representing specific cell functions close to ovulation, were highlighted.