Mount Nelson is a bay horse with a white star and stripe bred by the Cliveden Park Stud in Buckinghamshire. Mount Nelson was from the first crop of foals sired by Rock of Gibraltar who won seven Group 1 races in a row, including the 2000 Guineas. He has gone on to sire a number of other top racehorses, including Society Rock, Eagle Mountain, Varenar (Prix de la Forêt) and Samitar (Irish 1000 Guineas). Mount Nelson's dam, Independence, was a high-class racemare who won four races including the Matron Stakes and the Sun Chariot Stakes in 2001. She was descended from Home on the Range, the dam of the Epsom Derby winner Reference Point. Apart from Mount Nelson, Independence's best performer has been Monitor Closely, who won the Great Voltigeur Stakes and finished third in the St Leger Stakes.
As a yearling, the colt was consigned from the New England Stud to the Tattersalls sales at Newmarket. On 5 October he was bought for 330,000 guineas by the bloodstock agent Dermot "Demi" O'Byrne, acting on behalf of John Magnier's Coolmore organisation. Like many Coolmore horses, the details of Mount Nelson's ownership varied from race to race: he was sometimes listed as being owned by Derrick Smith, while in other races he was listed as the property of a partnership of Smith, Susan Magnier and Michael Tabor. The colt was trained throughout his racing career by Aidan O'Brien at Ballydoyle.
Mount Nelson did not compete in a race until late autumn, but then ran three times in a little over three weeks. On 6 October he started at odds of 5/2 in a seven furlong maiden race at Gowran Park, County Kilkenny and finished second of the fourteen runners behind the Dermot Weld-trained Treasure Map. In a similar event at the Curragh Racecourse sixteen days later, the colt started 2/1 favourite against twenty-eight opponents. Ridden by Seamie Heffernan, Mount Nelson established a clear lead approaching the final quarter mile and drew away from the field in the closing stages to win impressively by six lengths. Eight days after his win in the Curragh maiden race, the colt was moved up abruptly in class when he was sent to France to contest the Group One Criterium International over 1600 metres at Saint-Cloud Racecourse. He was coupled in the betting with his stable companion Yellowstone and went off at odds of 10.9/1, with the locally trained Spirit One being made the 3/5 favourite. Heffernan restrained Mount Nelson in the early stages before moving up to challenge the leaders in the straight. He took the lead approaching the last 200 metres and held off a sustained challenge of Spirit One to win by a short-head in a photo-finish, with Yellowstone in third. Despite the soft ground, the winning time of 1:41.3 was a new course record. Commenting on the performance, O'Brien said "Our decision to run Mount Nelson twice in the period of a week was justified, but it was a big risk. He's a lovely horse who will be even better next year when he should stay further." The trainer went on to mention the 2000 Guineas and the Poule d'Essai des Poulains as future targets, whilst bookmakers introduced him into the betting for the 2007 Epsom Derby at odds of 20/1.
Mount Nelson was being prepared for his three-year-old campaign when he sustained a serious injury to his left front foot. According to O'Brien the colt "tore off a shoe... and took half of his foot off with it". Both the hoof and bone were damaged, necessitating surgery and a long period of recuperation. He made his one and only appearance of the season at Newmarket Racecourse in October when he ran in the Champion Stakes. He started a 16/1 outsider and finished eleventh of the twelve runners, forty lengths behind the winner Literato.
On his return to racing as a four-year-old, Mount Nelson started odd-on favourite for the Mooresbridge Stakes at the Curragh in May, but was never in contention and finished sixth of the eight runners. A month later he showed improved form to finish third in the Prix du Chemin de Fer du Nord at Chantilly despite having difficulty obtaining a clear run in the straight. On 17 June, Mount Nelson returned to Group One level for the Queen Anne Stakes over one mile at Royal Ascot. Racing against leading milers he started at odds of 33/1 and finished fifth of the ten runners behind Haradasun, Darjina, Finsceal Beo and Cesare, beaten just over a length by the winner. For the second race in succession he encountered trouble in running, being "squeezed out" approaching the final furlong.