The Atlas San Juan Mission was conducted in February 2004 with the main objectives of observing the Urban Heat Island of San Juan, providing high resolution data of the land use for El Yunque Rain Forest and for calibrating remote sensors. The mission was coordinated with NASA staff members at Marshall, Stennis, Goddard, and Glenn. The Airborne Thermal and Land Applications Sensor (ATLAS) from NASA/Stennis, that operates in the visual and IR bands, was used as the main sensor and was flown over Puerto Rico in a Lear 23 jet plane. To support the data gathering effort by the ATLAS sensor, remote sensing observations and upper air soundings were conducted along with the deployment of a number of ground based weather stations and temperature sensors. This presentation focuses in the analysis of this complementary data for the Atlas San Juan Mission. Upper air data show that during the days of the mission the Caribbean mid and high atmospheres were relatively dry and highly stable reflecting positive surface lifted index, a necessary condition to conduct this suborbital campaign. Surface wind patterns at levels below 850mb were dominated by the easterly trades, while the jet stream at the edge of the troposphere dominated the westerly wind at levels above 500mb. The jet stream remained at high latitudes reducing the possibility of fronts. In consequence, only 8.4 mm of precipitation were reported during the entire mission. Observation of soundings located about 150 km apart reflected minimum variations of the boundary layer across the Island for levels below 850 meters and a uniform atmosphere for higher levels. The weather stations and the temperature sensors were placed at strategic locations to observe variations across the urban and rural landscapes. Time series plot of the stations’ data show that heavily urbanized commercial areas have higher air temperatures than urban and suburban residential areas, and much higher temperatures than rural areas. Temperature differences [dT(U-R)] were obtained by subtracting the values of several stations from a reference urban station, located in the commercial area of San Juan. These time series show that the UHI peaks during the morning between 10:00am and noon to an average of 4.5ºC, a temporal pattern not previously observed in similar studies for continental cities. It is also observed a high variability of the UHI with the precipitation patterns even for short events. These results may be a reflection of a large land use density by low level buildings with an apparent absence of significant heat storage effects in the urban areas, and the importance of the surrounding soil and vegetation moisture in controlling the urban tropical climate. The ATLAS data was used to determine albedo and surface temperature patterns on a 10m scale for the study area. These data were used to calibrate the spatial distribution of the surface temperature when using remote sensing images from MODIS (Moderate Resolution Imaging Spectroradiometer). Surface temperatures were estimated using the land surface temperature product MOD11_L2 distributed by the Land Process Distributed Active Archive Center (LP DAAC). These results show the maximum, minimum and average temperatures in San Juan and in the entire Island at a resolution of 1km. The information retrieved from MODIS for land surface temperatures reflected similar temporal and spatial variations as the weather stations and ATLAS measurements with a highest absolute offset of about 5ºC due to the differences between surface and air temperatures.