The objective of this study is to derive estimates of the mean seasonal variations in the Pacific to Indian Ocean throughflow transport using climatological data of the temperature/salinity fields and surface wind stress. A variable grid global general circulation model (GCM) with 1/6¿ resolution in Indonesian seas configured with ETOP05 bottom topography is utilized to diagnose the three-dimensional velocity field. An extensive set of sensitivity experiments is conducted to obtain estimates of the error bars. The computations show that Indonesian Throughflow (ITF) is maximum in boreal summer (13.9¿1.3 Sv) and minimum in boreal winter (7.5¿1.1 Sv). The annual mean ITF transport amounts to 11.5¿1.1 Sv (1 Sv=106 m3 s-1). These values are within the range of various estimations of ITF transport, and they agree in phase. The largest seasonal variations of the transport occur in the upper 175 m of the water column, exhibiting a 8 Sv amplitude of the seasonal cycle. This causes a substantial variability in the heat transport from the Pacific to the Indian Ocean. Its value increases from 0.4¿0.1 PW in January to 1.1¿0.1 PW in August (1 PW=1015 watts). In contrast to previous GCM-based studies, the annual mean transport is found to be more evenly distributed among the three major outlets from the Indonesian seas (Lombok, Ombai, and Timor Straits). The Luzon Strait inflow gives a considerable contribution to ITF. In winter the inflow of 6.3¿1.5 is distributed between the two outflows from South China Sea, which follow the routes through Karimata (4.4¿0.5) and Mindoro (1.9¿1.5 Sv) Straits. In summer the Karimata pathway is blocked, and the net inflow of 4.7¿0.6 Sv exits through the Mindoro Strait west of southern Luzon. The total contribution of the Luzon Strait inflow to the net ITF transport varies from 85% in boreal winter to 35% in summer, with an annual average value of ~50%. Cross-correlation analysis of the TOPEX/Poseidon monthly mean sea surface height (SSH) anomalies and the diagnosed transport anomalies demonstrates high correlation of the mean SSH difference between the regions in western Banda Sea and north of Luzon with the heat (0.96) and volume (0.91) transports. ¿ 2000 American Geophysical Union