Since the horse has a highly precocial reproductive strategy, most organs are functionally well developed at birth and thus, embryonic and fetal life is interesting. Data on the development of important organs are very limited. Here, we detailed macroscopically and histologically the equine digestive system, focusing on the first third of gestation. At 21 days, the oral cavity was an empty space, and the liver contained proliferating endodermal cells. At 25 days, a fusiform stomach and the pancreatic bud were present. At 28 days, a small tongue and the esophagus occurred. At 30 days, primary and secondary palates were developed, the liver contained cords of hepatocytes, and the pancreas was triangular. At 40 days, crypts had formed in the intestinal loops, cell differentiation was observed in the hepatic parenchyma, and the pancreas was elongated. Pancreatic acini and islets were observed in fetuses of 50 days and intestines were highly convoluted. Three segments of the pharynx were distinguishable at 75 days. At 105 days, the intestinal villi were wide with round tips; especially, the liver, stomach, and oral cavity showed key steps of anatomical and cellular differentiation in early fetuses, whereas other areas, such as pancreas or pharynx were still immature in the investigated phase. Pluripotency analysis using Oct4 showed initial intense staining in all of the digestive system tissues and a later decreased becoming restricted to specific cell layers. In conclusion, our data may contribute to perform a chronological reference of developmental events for approaches predicting pregnancy disorders in horses.