Complex Spectral Optical Tomography (CSOCT) in comparison to ordinary SOCT produces images free of parasitic mirror terms which results in double extension of the measurement range. This technique, however, requires the exact knowledge about the values of the introduced phase shifts in consecutive measurements. Involuntary object movements, which shift the phase from one measurement to another are always present in in vivo experiments. This introduces residual ghosts in cross-sectional images. Here we present a new method of data analysis, which allows determining the real phase shifts introduced during the measurement, and which helps to reduce the ghost effect. Two-dimensional cross-sectional in vivo images of human eye and skin obtained with the aid of this improved complex spectral OCT technique are shown. The method is free of polychromatic phase error originating from the wavelength dependence of the phase shift introduced by the reference mirror translation.