With increasing reliance on space-based platforms for global navigation and communication, concerns about the impact of ionospheric scintillation and total electron content fluctuations on these systems have became a high priority. In this paper, GPS transionospheric signals have been used to study the development of ionospheric phase fluctuations observed at Antarctic IGS permanent stations: McMurdo-MCM4, Casey-CAS1, Mawson-MAW1, Sanae-VESL, Syowa-SYOG and Davis-DAV1 in 2001. The use of the multi-station, multi-path observations of the GPS beacons has allowed the study of the time development of irregularities as a function of latitude and longitude of individual geomagnetic storms. The basic storms studied were those of March 19-20, March 31, April 9-11, June 16-17, and September 23, 2001. The rate of TEC (ROT) parameter was used to study the occurrence of TEC fluctuations. The results from studying these storms showed the unique nature of each storm. For the above five storms, data were available from three auroral stations (VESL, SYOG and MAW1) and from 61° to 70° Corrected Geomagnetic Latitude (CGL). In addition, data from three higher latitude polar stations (DAV1, MCM4 and CAS1) near 800 CGL are also analysed. Fluctuation effects, causing dramatic changes in total electron content – TEC, can have a different impact on GPS positioning accuracy (especially during phase ambiguity resolution). Bernese ver.4.2 software was used for the analysis of the GPS permanent data from Antarctic IGS stations. The analyses rely on studying the repeatability of vector co-ordinates. These vectors were investigated during the geomagnetic storms when the intensity of TEC fluctuations was more pronounced. The impact of TEC fluctuations in the high latitude ionosphere on GPS positioning accuracy has been discussed in terms of the total number of observations of doubledifferences (DD) and in the ratio of the total number of all ambiguities to unresolved ones.