A system of two scanning radiometers has been developed by the National Oceanic and Atmospheric Administration/Environmental Technology Laboratory and deployed on the NOAA R/V Ronald H. Brown during the Nauru99 cruise in the tropical western Pacific in June and July 1999. The system is composed of a high-quality temperature sensor and two independent, vertically scanning radiometers, measuring atmospheric and oceanic emission in the microwave (MW), and infrared (IR) regions. Both radiometers measure emission from a uniformly mixed atmospheric gas: oxygen for MW (60 GHz) and carbon dioxide for IR (14.2 μm). The high atmospheric absorption at these frequencies allows one calibration point from the horizontal atmospheric view using the in situ temperature sensor measurements as a reference. The signal at all other scan angles is scaled relative to that at the horizontal, resulting in a differential technique that is independent of calibration offset. This technique provides continuous and accurate estimates of boundary layer air temperature profile and air/sea temperature difference. The main advantage of this technique is that the water skin temperature can be measured at different optical depths without disturbing the skin layer (magnitude order of microns). We first compare radiometric data collected during the experiment with simulations obtained by atmospheric and oceanic radiative transfer models. We then use statistical inversion techniques to estimate air temperature profiles from upward looking measurements, based on an a priori data set of about 1500 ship-based radiosonde observations. For the “well-posed” problem of air/sea temperature difference estimation, we apply a physical retrieval algorithm to the downward looking measurements, accounting for air attenuation and sea surface roughness. Then we show retrieval results and evaluate the achieved accuracy. Finally, we compare radiometric estimates with in situ measurements, discussing similarities and discrepancies.