Context: Several studies have so far placed useful constraints on planetary atmospheric properties using transmission spectrsocopy, and in the case of HD209458b even the radial velocity of the planet during the transit event has been reconstructed opening a new range of possibilities. AIMS. In this contribution we highlight the importance to account for the orbital eccentricity and longitude of periastron of the planetary orbit to accurately interpret the measured planetary radial velocity during the transit. Methods: We calculate the radial velocity of a transiting planet in an eccentric orbit. Given the larger orbital speed of planets with respect to their stellar companions even small eccentricities can result in detectable blue or redshift radial velocity offsets during the transit with respect to the systemic velocity, the exact value depending also on the longitude of the periastron of the planetary orbit. For an hot-jupiter planet, an eccentricity of only e=0.01 can produce a radial velocity offset of the order of the km/s. Conclusions: We propose an alternative interpretation of the recently claimed radial velocity blueshift (~2 km/s) of the planetary spectral lines of HD209458b which implies that the orbit of this system is not exactly circular. In this case, the longitude of the periastron of the stellar orbit is most likely confined in the first quadrant (and that one of the planet in the third quadrant). We highlight that transmission spectroscopy allows not only to study the compositional properties of planetary atmospheres, but also to refine their orbital parameters and that any conclusion regarding the presence of windflows on planetary surfaces coming from transmission spectroscopy measurements requires precise known orbital parameters from RV.
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