The APE-THESEO campaign was held from 15 February to 15 March 1999 from the Seychelles in the western Indian Ocean. APE-THESEO stands for Airborne Platform for Earth observation — (contribution to) the Third European Stratospheric Experiment on Ozone. The campaign aimed to study processes controlling the low water content of the stratosphere, including the mechanisms of cloud formation in the tropical tropopause region, and transport processes, studied using measurements of long-lived trace gases and ozone. Two aircraft were used: the high-altitude research aircraft, M-55 Geophysica, which can fly up to 21 km, and the Falcon of the Deutsches Zentrum für Luft- und Raumfahrt, a tropospheric aircraft. Seven flights were performed, including the first simultaneous in situ and remote sensing of sub-visible cirrus clouds, the first interception of sub-visible cirrus using in-flight guidance from a path-finding aircraft, and guided descent of a high-altitude research aircraft into the anvil cloud at the top of a tropical cyclone. In this paper we describe the payload used, the objectives for each flight, and the meteorological conditions encountered. First results show that a new type of cloud, which we have dubbed ultra-thin tropical tropopause cloud (UTTC), has been observed frequently, and observed to cover areas of 105 km2. The frequent coincidence of the tropopause and hygropause implies that the western Indian Ocean played an important role in the dehydration of the lower tropical stratosphere during the season of the mission. UTTCs, sub-visible cirrus, and visible cirrus, have all been implicated in the observed dehydration. Tracer measurements indicate little mixing of stratospheric air into the upper tropical troposphere.