The coastal upwelling ecosystem of the Humboldt Current System off Peru and Chile exhibits strong interannual variability due to changes in the oceanographic conditions related to the El Niño (EN) Southern Oscillation. It is generally believed that major changes occur in the community structure and biological production of this system as a consequence of El Niño-La Niña periods. This paper presents a summary of the information available on the physical, chemical, and biological responses of the Chilean upwelling zone resulting from the strong 1997–1998 EN event. Oceanographic changes for the whole region included the intrusion of oceanic, low-nutrient, warmer, and more oxygenated waters into the coastal areas, with positive sea-surface temperature anomalies lasting until the winter of 1998. Off northern Chile, small-sized phytoplankton prevailed and chlorophyll-a fluctuated widely during most of the EN event, although inshore levels were consistently high. Zooplankton assemblages shifted to smaller species during the warm phase; the total biomass, however, did not change. Primary production rates and the vertical flux of carbon were not greatly affected. The total anchovy catch for 1997 held stable, reaching up to 1 million tons. In 1998, the catch decreased to 400,000 tons before recovering to 1.2 million tons in 1999 and 2000. Off central/southern Chile, the ‘normal’ seasonal regime (spring/summer benthic hypoxia) was replaced by oxygenation near the bottom and lower carbon input as a result of the EN event. Macrofaunal biomass increased significantly in the inshore sediments during the warm phase, then diminished in the following spring/summer period. The decreased macrofaunal biomass was associated with the disappearance of filamentous bacterial mats and increased benthic bioturbation. The overall productive capacity of the Chilean upwelling systems seems to have recovered rapidly after the EN decline, suggesting weaker ecological impacts than those observed in the seasons after the 1972–1973 and 1982–1983 events.