Abstract The Indonesian Throughflow (ITF) variability is assessed using a retrospective analysis of the global ocean based on the Simple Ocean Data Assimilation (SODA) experiment spanning the period 1950–99. A comparison between the 1983–95 observed ITF, and the simulated ITF suggests a reasonably accurate reconstruction of ocean circulation in the vicinity of the ITF during the available measurement record. A wavelet analysis shows that once the seasonal cycle is removed, the dominant variation of the ITF anomaly is an interannual oscillation with a period of about 4–7 yr. This interannual variability is significantly correlated with the El Niño–Southern Oscillation (ENSO) pattern, with the ITF lagging the ENSO cycle by 8–9 months. This suggests that large-scale tropical ocean–atmosphere interaction plays an important role in the interannual variability of the ITF. Regional upper-ocean heat content variability might also play a role in controlling interannual fluctuations of the ITF transport via geostrophic flows, though it could equally be ITF variations that establish heat content anomalies downstream of the Indonesian archipelago. The model heat transport associated with the ITF is in good agreement with the limited observational record available. Resultant variability in annual mean ITF heat transport is in the range 0.4–1.2 PW, which is significantly correlated with ITF and ENSO indices.