The mean and variable transport of the Indonesian Throughflow (ITF) are determined from full-depth velocity measurements in the three major exit passages of Lombok Strait, Ombai Strait, and Timor Passage from January 2003 through December 2006. Collectively, these passages convey the full-depth transport and stratification profile of the ITF from the Pacific Ocean to the Indian Ocean. To first order, the seasonal cycle of transport in the thermocline (∼100–150 m) in all three exit straits is dominated by regional monsoon forcing, with maximum ITF during the southeast monsoon. During the northwest monsoon, the surface transport relaxes in Timor and weakly reverses in Ombai and Lombok, so the main core of the ITF is subsurface. Below the thermocline, semiannual reversals occur in all three straits during the monsoon transitions in response to the passage of Indian Ocean wind-forced Kelvin waves. However, the reversals occur over different depth levels in each passage reflecting the influence of different sill depths along the coastal waveguide. The seasonal cycle of depth-integrated transports in Lombok and Ombai are strongly out of phase with Timor Passage, suggesting that the subthermocline flow is largely gated by these Kelvin waves. Despite the different seasonal transport phases, interannual anomalies in all three passages are remarkably similar, particularly during the strong positive Indian Ocean Dipole event in 2006 when transport in the surface layer is toward the Indian Ocean and reversed below. The deep reversals are likely in response to a series of Kelvin waves driven by anomalous zonal winds in the equatorial Indian Ocean. Total mean transport over the 3-year period is −2.6 Sv in Lombok Strait (i.e., toward the Indian Ocean), −4.9 Sv in Ombai Strait, and −7.5 Sv in Timor Passage. The transport in Timor Passage is nearly twice as large as historical estimates and represents half of the −15 Sv full-depth ITF transport that enters the Indian Ocean.