Nucleolar channel systems (NCSs), micron-sized organelles specific to nuclei of human endometrial epithelial cells (EECs), are robust markers of the midluteal phase under the apparent control of progesterone. To gain further insight into the role of progesterone in NCS formation, we quantitatively assessed their sensitivity to oral contraceptive pills (OCPs) using immunofluorescence-based detection of NCSs. Comparison of endometrial biopsies and serum progesterone levels on cycle day (CD) 10 and 20 (LH +6/7) of 6 naturally cycling women and 6 OCP users demonstrated that OCPs interfered with NCS formation on CD20, their natural peak presence. Although this confirmed prior observation based on electron microscopic sampling, OCPs unexpectedly induced limited but distinct amounts of NCSs already on CD10, when they are never present in natural cycles. Thus, OCPs can cause secretory changes in the endometrium during the proliferative phase. In a novel finding, robust NCS formation on CD20 was dependent on a 4 ng/mL progesterone threshold but did not correlate linearly with serum progesterone levels. Given the threshold being close to that serving as evidence for ovulation, NCSs can serve as ovulation markers.