Analyses of ocean current measurements from two moorings in the Makassar Strait (MAK-1, December 1996 to July 1998, and MAK-2, December 1996 to February 1998) with newly processed acoustic Doppler current profiler (ADCP) data provide a new estimate of transport and vertical velocity structure for this important passageway of the Indonesian Throughflow. The 7-month record of the MAK-1 ADCP and the 3-month record of the MAK-2 ADCP, nominally set at depths of 150 m, are extrapolated to the end of the mooring period using a surface layer relationship to the shallowest current meter at 200 m and to the regional winds. The southward transport within Makassar Strait is confined for the most part to the upper 750 m, above the blocking topographic sill of Makassar Strait. The transport maximum occurs within the thermocline (100--300 m). After the temporal mean flow has been removed, the vertical structure of the along channel flow in the upper 750 m is decomposed using the empirical orthogonal function (EOF) method. The first two modes contain 91% of the total variance. For the entire mooring period, the total depth-integrated transport was 8.1 ¿ 1.5 Sv (Sv = 1 ¿ 106 m3/s), with 7.9 ¿ 1.2 Sv for calendar year1997. During the peak of 1997/1998 El Ni¿o from September 1997 to mid-February 1998, the first mode time series displays northward flow, enhancing the vertical shear within the thermocline and reducing the mean throughflow to 4.6 ¿ 0.9 Sv.