After Ögedei's death in 1241, it was five years before the next khagan (great khan) was elected; the next khagan was Güyük Khan, oldest of Ögedei's sons. Who ran the empire for those five years? Power immediately passed to Möge Khatun (khatun = queen), perhaps Ögedei's favourite wife (and formerly a concubine of Chinggis), who ruled as regent. However, it was only a few months before Ögedei's second wife, Töregene Khatun, forced her out of power and took over as regent, supported by Chagatai (Chinggis's second son) and her sons (including Güyük, Ögedei's oldest son).

Ögedei's preferred successor had been his favourite son, Köchü, until his death in 1237 (fighting against the Song). Next, Ögedei nominated Köchü's son Shiremun as his successor. While Ögedei could and did name his preferred successor, the khagan was traditionally elected, and Shiremun could not become khagan without that election. Thus, the regency. Töregene does not appear to have been in a hurry to hold the election, and was content to rule as regent, going so far as to take the title "Great Khatun", and showing signs of wanting to rule until her death. This did not endear her to rivals for power (including her son Güyük). She further increased her unpopularity by replacing Ögedei's ministers with her own, including her favourite Fatima, originally taken captive in Mashhad (today Iran's second largest city).

Opposition to Töregene grew, led locally by Temüge, the youngest brother of Chinggis, and remotely by Batu, Khan of the Golden Horde. Töregene agreed to finally allow the electoral assembly (the kuriltai) to meet and elect the next khagan; she had gathered enough support to ensure the election of Güyük, and she hoped to continue as the power behind the throne. Güyük was duly elected in 1246, and became khagan. Töregene's hope of continuing to wield power were not realised. Fatima was accused of witchcraft, and executed in 1246, and Töregene's people were purged from the government. Töregene herself died, assumed to be murdered by order of Güyük in the next year or 2.

Güyük's election brought the empire to the brink of civil war, with Batu leading the opposition. Batu and Güyük gathered their armies. Güyük's army was supposedly gathered for the conquest in the Middle East, but was believed to be aimed at Batu. Güyük died (in 1248) before the armies got close to meeting, probably of disease, but there was suspicion that either Batu or Sorghaghtani, the widow of Chinggis's son Tolui, had arranged for him to be poisoned. After the death of Güyük, Sorghaghtani worked to secure the throne for her son Möngke. Möngke went to Batu, and they came to a gentlemanly agreement: Batu would support Möngke's election, and would acknowledge Möngke as his superior. Möngke would, in turn, essentially give Batu autonomy. Batu called a mini-kuriltai in Ala Qamaq (location unknown, but in the west), which elected Möngke. To strengthen his legitimacy, a second kuriltai was called in Mongolia in 1251, again electing Möngke.

Möngke ruled as khagan for longer than Güyük, but not for very long, dying in 1259 (probably of disease) fighting the Song in Sichuan. The next khagan was his younger brother Kublai.

Two notable European visitors to the Mongol court recorded elements of these events. The first, Giovanni da Pian del Carpine AKA John of Plano Carpini, was present for the election and enthronement of Güyük. After Güyük's enthronement, Carpini's party met with Güyük, and invited him to become a Christian (he refused). They returned to Europe with a letter from Güyük to the Pope. The second, William of Rubruck, arrived in Karakorum at the end of 1253, meeting with the khagan, Möngke, in the following January. He stayed for about 6 months, and then returned to Europe, with a letter from Möngke to King Louis IX of France. Both Carpini's and Rubruck's accounts of their visits to Mongolia have survived. Rubruck gives a second-hand account of Shiremun's revolt in 1251 against Möngke, including the execution of Shiremun (other sources disagree, stating that Shiremun was sent to China with the army). Möngke's letter to Louis IX shows a remarkable willingness to bare Mongol dirty laundry in public:

Your envoys arrived at Keu Chan's [Güyük Khan] residence after his death. Camus [Güyük's widow, Oghul Qaimish], his wife, sent you nasic cloth and a letter. But as for knowing the business of war and the affairs of peace, subduing the wide world and discerning how to act for the best - what could that worthless woman, lower than a bitch, have know of this?

Rubruck commented on this passage:

Mangu [Möngke] told me with his own lips that Camus was the worst of witches, and that with her sorcery she had destroyed her entire family.

Oghul Qaimish was officially executed as a witch in 1251, but the main reason was her support for Shiremun's revolt. It doesn't seem that Oghul Qaimish's letter to Louis IX contained anything outrageous that Möngke needed to disown. In response to discussions for an alliance against the Muslim states in Egypt and Syria, she demanded the submission of Louis IX and France to Mongol authority, which was standard Mongol diplomacy.