Global Positioning System (GPS) Radio Occultation (RO) data are the currently only satellite data that maintain the traceability to absolute standard of units (SI traceability). By flying a GPS receiver on a low earth orbit (LEO), GPS RO is the first technique to provide the global RO phase delay data, which is traceable to the international standard of time. Raw RO observations and precise positions and velocities of GPS and low-Earth orbiting (LEO) satellites can be used to derive accurate atmospheric bending angle, refractivity, geo-potential height, and temperature profiles. However, while the fundamental phase delay observed from the GPS RO technique is synchronized to the ultra-stable atomic clocks on the ground, the retrieved RO variables (e.g., refractivity, geo-potential height, and temperature profiles) are not. The quality and accuracy of the retrieval results may vary when different assumptions, filtering, initializations, and implementations in the excess phase processing and inversion procedures are used. To examine the suitability of GPS RO observations as a climate benchmark dataset, this study aims at quantifying the structural uncertainty in GPS RO-derived vertical profiles of bending angle, refractivity, temperature, and geo-potential height, and measured trends obtained from atmospheric excess phase processing and inversion procedures. Seven years (2002–2008) of the matched retrieved profiles from the experiment aboard the German satellite CHAMP (CHAllenging Minisatellite Payload) generated by six RO operational centers were compared. Results show that the absolute values of fractional refractivity anomalies among the centers are in general ≤ 0.2% from 8 to 25 km altitude and the absolute values of temperature anomalies are less than 0.3 K in the same vertical layer. Results of time series comparisons of retrieval anomalies will also be presented. We seek to find out the sources of uncertainty for differences in zonal average anomalies and time series and trend analysis for all RO derived variables.