In cattle, endometrial gene expression during the first 2 weeks after fertilization is different in cattle that conceive compared with those that fail to conceive. The potential selection of animals based on endometrial marker expression before the day of embryo transfer may improve the efficiency of bovine embryo transfer. This study aimed to evaluate the morphological and molecular changes induced by endometrial biopsy in cycling tropically adapted beef cattle. In both experiments, a single biopsy was performed on the horn ipsilateral to the corpus luteum using a circular cup biopsy forceps. The uterus was collected after slaughter, and sections were taken adjacent to the biopsy site. Five heifers were not biopsied and acted as controls. In Experiment 1, presynchronised heifers (n = 10) were biopsied on Day 7 post-oestrus (B7) and then resynchronised with cloprostenol (Estromil®, 250 μg IM) to induce oestrus (O), 2 to 3 days after injection. At Day 7 post-oestrus (D7), the reproductive tracts were collected, 10 days after biopsy (B7-O-D7). In Experiment 2, presynchronised heifers (n = 7) were biopsied on Day 4 post-oestrus (B4), and reproductive tracts were collected 3 days later (B4-D7). A quantitative scoring system was used to define histological appearance of the endometrium (1 to 25; above 16 indicates endometritis). The RNA expressions of interleukin-1-β (IL-1β) and transforming growth factor-β (TGF-β) were measured by quantitative real-time PCR (qRT-PCR). Macroscopic examination showed the uterus collected from B7-O-D7 heifers exhibited a focal, well demarcated, dark red discoloration of the endometrium (4/10) with no evidence of the biopsy site found in the remaining heifers (6/10). The biopsied uteri from B4-D7 heifers revealed no macroscopic evidence of the biopsied site (4/7), serosa congestion (2/7), and one case where a severe endometrial haemorrhage was evident (1/7). Histologically, the overall mean score was not indicative of endometritis. The RNA expression showed up-regulation of both IL-1β and TGF-β in both B7-O-D7 and B4-D7 heifers compared with non-biopsied heifers and significantly higher expression of IL-1β in B4-D7 than B7-O-D7 (P = 0.031, P