The purpose of this thesis is to examine the effects of magnetic activity on the low latitude F-region thermospheric winds. The F-region (120-1600 km) is a partially ionized medium where O+ and O are the major ion and neutral species, respectively. The thermospheric winds at these altitudes are driven primarily by pressure gradient forces resulting from the solar heating during the day and cooling at night. For this study, we use measured Fabry-Perot Interferometer (FPD winds at Arequipa (16.5°S, 71.5°W) and measured FPI and Incoherent Scatter Radar (ISR) winds at Arecibo (18.6°N, 66.8°W). Previous wind studies at Arequipa and Arecibo concentrated on the climatological wind patterns highlighting solar cycle effects and seasonal variations; however, these studies did not address the effects of magnetically disturbed conditions on the seasonal averaged winds. To properly investigate storm time effects on the neutral winds, we must first investigate solar cycle effects on the seasonal averages during magnetically quiet (Kp < 3) conditions. This study will include a detailed analysis of solar cycle effects on the seasonally averaged winds for Arequipa and Arecibo. In addition to the wind averages, we used cubic splines to fit the average wind profiles and to provide better comparisons with modeled results. We also performed a study on the airglow emission heights using both Jicamarca and Arecibo electron density profiles. This established the height which we will use to compare our experimental data with the model winds. To investigate magnetic activity effects on the FPI and ISR winds, we used three magnetic activity cases which cover all storm time scenarios. These magnetic activity cases are the extended quiet, short-term disturbed, and extended disturbed conditions. The first case, the extended quiet, is the condition where the previous and short term magnetic activity is quiet (12 hour Kp ≤ 3 and the Kp ≤ 3). The short-term disturbed case is defined for the condition where the previous magnetic activity is quiet (12 hour Kp ≤ 3) and then becomes disturbed (Kp ≤ 3). Last, we considered the case where previous and short-term magnetic activity are disturbed (12 hour Kp ≤ 3 and the Kp ≤ 3). Our last objective is to use our data to validate the predictions from the Thermosphere/Ionosphere General Circulation model (TIGCM93) and the Horizontal Wind Model (HWM93). This study should further our understanding of the physical processes which produce the low latitude quiet and disturbed winds. The TIGCM93 is a first principal model and the HWM93 is an empirical model based on ground-based and satellite measurements. The main advantage of using the TIGCM93 is the ease of studying the dynamics of ionospheric phenomena by simply changing various model inputs, while the HWM93 allows us a comparison between our experimental wind data sets with the established climatology of the winds over Arequipa and Arecibo.