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Aim Pulmonary hypertension (PH) is a severe complication of congenital diaphragmatic hernia (CDH). Transforming growth factor-β (TGFβ) signaling is suggested to be involved in PH development by regulating embryonic angiogenesis, cell proliferation, and cell differentiation. Altered TGFβ signaling has been demonstrated in experimental CDH lungs. Elastin microfibril interfacer 1 (Emilin-1) is an extracellular matrix glycoprotein expressed in endothelial and vascular smooth muscle cells and known to regulate TGFβ processing and arterial diameter. We designed this study to investigate the pulmonary vascular expression of Emilin-1 in nitrofen-induced CDH rats.Materials and Methods Following ethical approval (REC913b, REC1103), time-pregnant Sprague Dawley rats received nitrofen or vehicle on gestational day 9 (D9). Fetuses were sacrificed on D21 and divided into CDH group and control group. Quantitative real-time polymerase chain reaction (n = 11 each group), Western blot analysis, and confocal microscopy were used to determine the gene and protein expression of Emilin-1.Main Results Relative Emilin-1 messenger RNA (ribonucleic acid) levels were significantly downregulated in CDH lung tissue compared with controls (CDH: 0.043 ± 0.003; control: 0.067 ± 0.004; p < 0.001). Western blotting confirmed the decreased pulmonary Emilin-1 protein expression in CDH lungs. Confocal microscopy demonstrated a markedly diminished expression of Emilin-1 in the CDH pulmonary vasculature compared with controls.Conclusion To our knowledge, this study demonstrates for the first time a decreased Emilin-1 gene and protein expression in the pulmonary vasculature of nitrofen-induced CDH. Emilin-1 deficiency through its interaction with TGFβ may result in abnormal vascular remodeling resulting in PH in this model.