In this paper, we discuss the development of the inversion algorithm for the GOMOS (Global Ozone Monitoring by Occultation of Star) instrument on board the Envisat satellite. The proposed algorithm takes accurately into account the wavelength-dependent modeling errors, which are mainly due to the incomplete scintillation correction in the stratosphere. The special attention is paid to numerical efficiency of the algorithm. The developed method is tested on a large data set and its advantages are demonstrated. Its main advantage is a proper characterization of the uncertainties of the retrieved profiles of atmospheric constituents, which is of high importance for data assimilation, trend analyses and validation.