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Durante la era Cenozoica cuatro intervalos de tiempo: el Eoceno temprano (~50 Ma), el Plioceno temprano (~5-3 Ma), el ultimo glacial máximo (~20 ka) y el Holoceno (<10 ka), han sido examinados en detalle en un esfuerzo para entender el fenómeno de El Niño bajo diversas condiciones frontera. Para el Eoceno y Plioceno tempranos se argumenta la posible existencia de condiciones permanentes tipo - El Niño, mientras que para el ultimo glacial las evidencias de condiciones tipo - El Niño o La Niña son aun contradictorias. Solo para el Holoceno (después de ~6.6 ka) se reconoce el inicio del fenómeno de El Niño en su frecuencia actual, como también su posible relación con mecanismos forzantes como la radiación solar y la actividad volcánica. Se discuten las evidencias paleoceanográficas y continentales del fenómeno, así como también su posible relación con pulsos orogénicos en el norte de Suramérica.
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