Toll-like receptor 9 (TLR9) has been found to be the main receptor to respond to bacterial DNA in a wide variety of species. Recent work has shown that TLR9 is expressed in a diverse set of cells within the lung. However, much of this data has been centered on human and mouse cell culture lines or primary cultures and very little is known of TLR9 expression in intact lung, especially that of the horse. Here we show that TLR9 is expressed in the lungs of horses in a wide variety of cells. In particular, we note expression in pulmonary intravascular macrophages (PIMs), alveolar macrophages, bronchial epithelial cells, and type-II cells amongst others. Immunogold electron microscopy localized TLR9 in nuclei, cytoplasm, and plasma membrane of various lung cells. The data also show that E. coli lipopolysaccharide significantly increased expression of TLR9 mRNA in lungs and the number of cells in the lung septa that were positive for TLR9 protein. Protein expression was seen in airway epithelium, vascular endothelium, and inflammatory cells in blood vessels. Intravenous administration of gadolinium chloride, which depletes macrophages, before the lipopolysaccharide treatment significantly inhibited the LPS-induced increase in TLR9 mRNA in the lungs of the horses. We conclude that TLR9 is expressed in lung cells including PIMs and that the lipopolysaccharide treatment increases TLR9 mRNA expression. The increase in TLR9 mRNA is eliminated by depletion of PIMs, implicating these cells as a major source of TLR9 in the equine lung.