Intravital microscopy of orthotopic lung tissue is technically demanding, especially for repeated investigations. Therefore, we have established a novel approach, which allows non-invasive repetitive in vivo microscopy of ectopic lung tissue in dorsal skinfold chambers. Syngeneic subpleural peripheral lung tissue and autologous endometrium (control) were transplanted onto the striated muscle within dorsal skinfold chambers of C57BL/6 mice. Grafts were analysed by intravital fluorescence microscopy over 14 days. Angiogenesis occurred in the grafts on day 3, as indicated by sinusoidal microvessels on the grafts' edges with very slow blood flow, perifocal oedema, and haemorrhage. By day 10, lung transplants were completely revascularized, exhibited a dense network of microvessels with irregular diameters, chaotic angioarchitecture, and high blood flow. Compared to lung tissue, endometrial grafts contained a structured, glomerulus-like vessel architecture with lower blood flow. Despite missing ventilation, hypoxic vasoconstriction of the lung tissue arterioles occurred. In contrast, endometrium tissue arterioles dilated during hypoxia and constricted in hyperoxia. This demonstrates that ectopic lung grafts keep their ability for organ-specific hypoxic vasoconstriction. These findings indicate that our approach is suitable for repetitive in vivo pulmonary microcirculation analyses. The high blood flow and hypoxia-induced vasoconstriction in lung grafts suggest a physiological intrinsic vasoregulation independent of the recipient tissue.