Ruben Weber-Jackson, from Beverley, Yorkshire, was suffering from restricted breathing because of the holes.
Now, during two major operations, they have been repaired – using tissue from a cow’s heart – and he can breathe normally.
When Ruben was born last year, his parents thought he was a happy and healthy baby.
His mother Petra, 29, said: ‘He was pink and everything seemed perfect, really. But in hindsight, there were probably a few little signs, but nothing significant that made us think there was a real problem.
‘I remember saying he was such an easy baby who sleeps a lot and was very calm. He also had swollen eyes and there is one photo we took where his lips looked slightly purple.’
But when he was two weeks and two days old, she noticed his breathing was unusual.