The human endometrium is a dynamic tissue that undergoes molecular and cellular changes in preparation for embryo implantation in every menstrual cycle. The luminal epithelium (LE), the first cell layer of the endometrium that would interact with an implanting embryo, must transform from a non-receptive to a receptive state for the initiation of embryo implantation. The other epithelial sub-type, the glandular epithelium (GE), is located inside the tissue on the glands and would interact with the embryo only after it has entered the endometrium. Our previous studies have indicated that during the establishment of endometrial receptivity, genes in LE are regulated differently from GE. However, research in the field has largely overlooked the difference between LE and GE and they are often regarded as one entity, to date it is not well understood how these two sub-types of epithelial cells differ in gene expression in general and when remodelling for receptivity. In this study, we aimed to establish the global transcriptomic profiles of human endometrial LE and GE across the menstrual cycle. Laser capture microdissection was used to dissect LE and GE from endometrial tissues biopsied in the proliferative (non-receptive) and mid-secretory (receptive) phases of the menstrual cycle, total RNA was isolated from these cells and then analysed by RNAseq. Our data showed that the majority of genes were expressed similarly between LE and GE, however, many genes were transcribed very distinctly between LE and GE cycle-stage dependently as well as independently, and many were regulated very differently between LE and GE for receptivity. This is the first study to comprehensively analyse the global gene expression of LE and GE in the human endometrium, and our data provide new and important insights into the understanding of endometrial epithelial sub-types and their distinct remodelling in the establishment of receptivity.