Endometrial health is vital for the reproductive efficiency of broodmares and accurate diagnostic testing is crucial for directing the best treatment options and outcomes. Confocal laser endomicroscopy (CLE) is an endoscopic technique for obtaining in-vivo, real-time microscopic imaging of tissues using a fiber optic probe. CLE relies on induced tissue fluorescence and fluorescein sodium, given intravenously, is the contrast agent most used in human medicine. This study aimed to determine the feasibility of CLE for imaging equine endometrium and determine a standard dose of fluorescein sodium to achieve optimal cellular imaging. In-vivo CLE was performed on 44 mares, and the images were compared with routine histopathological analysis of endometrial biopsies. No adverse reactions occurred after IV fluorescein sodium administration and a dose of 4mg/kg was established (0.04mL/kg of 10% fluorescein sodium solution) to achieve optimal image contrast. CLE enabled multiple regions of the endometrium to be assessed quickly. Distinct tissue architecture patterns could be appreciated using CLE, and the luminal epithelium could be assessed for integrity (ulceration) and exocytosed inflammatory cells. Endometrial gland distribution, density, shape, and epithelial height were evaluated. Blood vessels were clearly outlined, and inflammatory cells and fibrosis were discernable within the interstitium. Image quality varied between mares, and the stage of oestrous cycle may have been a factor of influence. This novel imaging modality enables collection of “virtual” biopsies and facilitates critical assessment of multiple regions of the uterus compared with the standard histopathologic assessment of a single random tissue biopsy.