Abstract. Sea ice freeboard derived from satellite altimetry is the basis for estimation of sea ice thickness using the assumption of hydrostatic equilibrium. High accuracy of altimeter measurements and freeboard retrieval procedure are therefore required. As of today, two approaches for estimation of the freeboard using laser altimeter measurements from Ice, Cloud, and land Elevation Satellite (ICESat), referred to as tie-points (TP) and lowest-level elevation (LLE) methods, have been developed and applied in different studies. We reproduced these methods in order to assess and analyze the sources of differences found in the retrieved freeboard and corresponding thickness estimates of the Arctic sea ice as produced by the Jet Propulsion Laboratory (JPL) and Goddard Space Flight Center (GSFC). For the ICEsat observation periods (2003–2008) it is found that when applying the same along-track averaging scales in the two methods to calculate the local sea level references the LLE method gives significantly lower (by up to 15 cm) sea ice freeboard estimates over thick multi-year ice areas, but significantly larger estimates (by 3–5 cm in average and locally up to about 10 cm) over thin first-year ice areas, as compared to the TP method. However, we show that the difference over first-year ice areas can be reduced to less than 2 cm when using the improved TP method proposed in this paper. About 4 cm of the difference in the JPL and GSFC freeboard estimates can be attributed to the different along-track averaging scales used to calculate the local sea level references. We show that the effect of applying corrections for lead width relative to the ICESat footprint, and for snow depth accumulated in refrozen leads (as it is done for the last release of the JPL product), is very large and increase freeboard estimates by about 7 cm. Thus, the different along-track averaging scales and approaches to calculate sea surface references, from one side, and the freeboard adjustments as applied in the TP method used to produce the JPL dataset, from the other side, are roughly compensating each other with respect to freeboard estimation. Therefore the difference in the mean sea ice thickness found between the JPL and GSFC datasets should be attributed to different parameters used in the freeboard-to-thickness conversion.