The subsurface connections between the Equatorial Current System (ECS) and the Peru Current System (PCS) between 1999 and 2005 are investigated with a primitive-equation, eddy-resolving regional model that is forced with realistic atmospheric and lateral oceanic conditions. Specific attention is given to the 1999-2000 La Nia and the 2002-2003 El Niño. The model's skill is assessed through a comparison with satellite-derived sea level anomalies and in situ sea surface temperature time series. The model reproduces fairly well the known dynamics of the region for climatological conditions, and the numerical solution obtained for the particular 1999-2000 and 2002-2003 events presents patterns rather typical of cold and warm phases of El Niño-Southern Oscillation (ENSO). Eulerian and Lagrangian diagnoses are used to derive relevant information about the density and velocity vertical structures of the ECS and the PCS. The transports of the major currents in the region are shown to differ a lot between the 1999-2000 La Nia and the 2002-2003 El Niño. The equatorial subsurface currents transfer significantly more water into the eastern tropical Pacific during La Nia than during El Niño, whereas the Peru-Chile Undercurrent (PCUC) carries more water during El Niño. The equatorial subsurface currents, and especially the primary Southern Subsurface Countercurrent, contribute to 80% of the PCUC transport during the 1999-2000 cold phase. This ratio falls down to only 20% during the 2002-2003 warm phase. Copyright 2011 by the American Geophysical Union.