The Alai Valley of Kyrgyzstan is an east-west-oriented intramontane basin along the northern perimeter of the India-Eurasia collision zone. It is the vestige of a once continuous sedimentary basin linking the Tadjik and Tarim depressions to the west and east, respectively. The valley is bounded to the south by the active Main Pamir Thrust (MPT) of the Trans Alai, and the Alai Range of the southern Tien to the north. West of 073°E, the MPT is divided into 2 segments, linked by a NW-oriented transfer zone with dextral transfer faults and thrust faults. We present a series of N-S structural cross-sections based on field observations and seismic reflection data in order to better understand space and time relationships of progressive basin closure. The Paleozoic basement of the Ala Valley and surrounding regions consists of Devonian limestones and marbles and Carboniferous metasedimentary rocks. It is unconformably overlain by Jurassic conglomerates, sandstones, and argillite interbedded with gypsum and coal. In the Tien Shan, lower Cretaceous rocks overlie basement or Jurassic rocks and mainly include red conglomerate, carbonaceous sandstones, and mudstones, followed by gypsum, mudstone and limestone. These units are overlain by Paleogene gypsum, dolomite, and limestone, which are separated from lower Neogene conglomerate by an angular unconformity. However, in the southwest, along the Trans Alai mountain front, an approximately 3-km-thick sequence of chronologically poorly constrained Neogene cross-bedded red sandstones and mudstones is conformable with Paleogene strata. Upsection the sequence is overlain by 1000-m-thick conglomeratic molasse deposits in front of the Pamir thrust systems. Dip sections of seismic reflection profiles show that the Alai Valley is an asymmetric full-ramp basin bounded by S- and N-vergent thrust systems with the basin deepening toward the south. Shortening in the Tien Shan began in early Neogene time. This is clearly documented by the shift from marine to continental sedimentation and by the marked angular unconformity separating Paleogene and Neogene strata, where the Paleozoic basement rocks were thrusted over the Meso-/Cenozoic cover along a decollement in the Paleogene gypsum. The external part of the Trans Alai range is defined by a stack of steeply southward dipping thrust sheets involving Cretaceous and Paleogene units with thrusts detached along Paleogene gypsum layers. These rocks overthrust folded Neogene syntectonic conglomerates. For example, west of the Minjar drainage at about 072° 40°E, a tight asymmetric E-W trending anticline is truncated at the range front by the active MPT, and interpreted as a fault-propagation fold, as the thrust steps northward and cuts through the Neogene deposits displacing several generations of Quaternary pediments. This attests to the recency of deformation along this mountain front which contrasts sharply with the inactive southern Tien Shan. In addition, these observations show that the closure of the Alai Valley is accomplished by progressive N-directed thrusting.