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On 19 September 2008, a quench occurred in about 100 bending magnets in sectors 3-4, causing loss of approximately six tonnes of liquid helium, which was vented into the tunnel, and a temperature rise of about 100 kelvins in some of the affected magnets. Vacuum conditions in the beam pipe were also lost.[27] Shortly after the incident CERN reported that the most likely cause of the problem was a faulty electrical connection between two magnets, and that - due to the time needed to warm up the affected sectors and then cool them back down to operating temperature - it would take at least two months to fix it.[28] Subsequently, CERN released a preliminary analysis of the incident on 16 October 2008,[29] and a more detailed one on 5 December 2008.[9] Both analyses confirmed that the incident was indeed initiated by a faulty electrical connection. At most 29 magnets have been damaged in the incident and will have to be repaired or replaced during the winter shutdown.

In the original timeline of the LHC commissioning, the first "modest" high-energy collisions at a center-of-mass energy of 900 GeV were expected to take place before the end of September 2008, and the LHC was expected to be operating at 10 TeV by the time of the official inauguration on 21 October 2008.[30] However, due to the delay caused by the above-mentioned incident, the collider will not be operational again until summer 2009.[8][9]