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The Olympic, European and Commonwealth champion was set to compete in the long jump following his win and indoor personal best performance at the Sainsbury’s Indoor Grand Prix last weekend.
Rutherford has now decided to let his body recover from the competition fully and concentrate on the outdoor season ahead.
Rutherford said: "While I would have loved to compete at the European Indoor Championships, I have decided to remove myself after a long deliberation.
"My body still hasn't fully recovered from the Grand Prix and with an incredibly important summer coming up where I intend on giving it my all to win the World Championships in Beijing I've decided to keep my focus purely on the summer season.
"I wish all of the British athletes competing in Prague the very best of luck, and I will be a fan cheering them on from home."
Elsewhere Rory Evans has withdrawn from the men’s 4x400m with an injury, and will be replaced by Alex Boyce (Paul Boyce).
UKA Athletics – News
