Although the El Niño/Southern Oscillation phenomenon is the most prominent mode of climate variability¹ and affects weather and climate in large parts of the world, its effects on Europe and the high-latitude stratosphere are controversial^2,3,4,5. Using historical observations and reconstruction techniques, we analyse the anomalous state of the troposphere and stratosphere in the Northern Hemisphere from 1940 to 1942 that occurred during a strong and long-lasting El Niño event. Exceptionally low surface temperatures in Europe and the north Pacific Ocean coincided with high temperatures in Alaska. In the lower stratosphere, our reconstructions show high temperatures over northern Eurasia and the north Pacific Ocean, and a weak polar vortex. In addition, there is observational evidence for frequent stratospheric warmings and high column ozone at Arctic and mid-latitude sites. We compare our historical data for the period 1940–42 with more recent data and a 650-year climate model simulation. We conclude that the observed anomalies constitute a recurring extreme state of the global troposphere–stratosphere system in northern winter that is related to strong El Niño events.

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