The tests at the European Organisation for Nuclear Research (CERN) came after a sweeping two-year revamp of the collider and will help scientists to study fundamental particles, the building blocks of all matter, and the forces that control them.
During its next run, researchers will look for evidence of "new physics" and probe "supersymmetry" - a theoretical concept informally dubbed Susy; seek explanations for enigmatic dark matter and look for signs of extra dimensions.
CERN said everything went according to plan at the giant lab, a 27-kilometer (17-mile) ring-shaped tunnel straddling the French-Swiss border.
During what it dubbed as its "Season Two", the LHC will in the course of the next three years strive to fill gaps in the so-called "Standard Model" - the mainstream theory of how the visible Universe was created but which does not explain dark matter.
"We have seen the first data beginning to flow. Let's see what they will reveal to us about how our universe works," he said.
"It's not going to happen tomorrow, be patient," he said, as scientists monitoring the event broke into sustained applause and uncorked champagne.
On May 20, the LHC broke the record for energy levels colliding protons at 13 TeV - or 99.9 per cent of the speed of light - for the first time.
The LHC's previous highest energy for collisions was eight TeV, reached in 2012 before it closed for the upgrade.
The LHC was used to prove the existence of the Higgs Boson, a discovery that earned the 2013 Nobel physics prize for two of the scientists who had theorised the existence of the Higgs back in 1964.
The LHC allows beams containing billions of protons to shoot through the massive collider in opposite directions.
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