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At the end of his racing career, Hernando was retired to become a breeding stallion at the Lanwades Stud in Newmarket. He sired numerous major winners including Sulamani, Look Here, Gitano Hernando (Singapore Airlines International Cup), Casual Conquest (Tattersalls Gold Cup) and Holding Court (Prix du Jockey Club) He was also a successful sire of National Hunt horses including State Of Play (Hennessy Gold Cup), Sacundai (Aintree Hurdle), Cape Tribulation (Cotswold Chase), Conquisto (Old Roan Chase) and No Refuge (RSA Chase). He was retired from stud duty in 2011 and died of a heart attack in February 2013. The stud's owner Kirsten Rausing described Hernando as "a most charming character, always kind and co-operative, and he is very sadly missed by us all at Lanwades". Hernando was buried at Lanwades alongside his fellow stallion Selkirk who had died a month earlier.