Scott has been plagued by fatigue in recent games, prompting the medical staff to send him for tests which revealed he had a lung infection.
Further examinations showed the player had a heart problem, which could have had fatal consequences at any time during his 13-year career.
Doctors told him he would no longer be able to play competitive sport, and has to restrict any physical activity.
Orient boss Martin Ling said: "I's a massive loss to the club but it¹s an even bigger loss to Andy Scott.
"I'm more interested in Andy Scott the person than the footballer right now.
"No-one expected this. He's been struggling for the last three or four games and we put it down to a lung infection, but more tests have shown it was his heart. He's very lucky to still be here."