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Light pipes transmit daylight into building interiors. Their installation into thermally insulated roofs of low energy buildings can be a problem because of thermal bridges and condensation problems. This article is focused on a CFD simulation thermal analysis that includes four variations of light pipes with a segment of a flat roof. Common light pipes with a hollow light guiding tube were compared to special light pipes containing an additional glass unit located inside the tube. The additional glass units increase thermal resistance and reduce condensation risks of the light guiding systems. The light pipes were compared in two different simulation models run in ANSYS Fluent software and the CalA program. Temperature profiles and air flow patterns of the cross sectional profiles of the light pipes served to determine the total heat transmittance and heat losses of the studied light pipes installed in a segment of a thermally insulated flat roof. The paper compares simplified 2D rotational–symmetrical numerical model based on the thermal diffusion equation with the complex 3D CFD numerical simulation. The results confirm that the simplified 2D numerical model is suitable for the thermal evaluation of the light pipes containing an additional glass unit, too. The additional glass unit with the triple glass improves thermal resistance up to 88% in case of light pipe with diameter 600 mm and reduces optical transmittance to 28%. [ABSTRACT FROM AUTHOR]