David Harris, 63, who worked at Hilltop Special Boarding School, Stevenage, was found dead in bed at his Plymouth home after police forced their way inside.
No apparent cause of death has yet been established.
Mr Harris failed to appear for trial on Tuesday charged with sexual offences on five boys between 1972 and 1990.
Mr Harris had been due to appear at Luton Crown Court charged with offences against the boys, aged seven and eight at the time.
When he failed to turn up at court a bench warrant was issued by Judge Richard Foster.
Then, on Wednesday, the news reached the court that police who had entered his home in Knighton Road had discovered a body.
Judge Foster adjourned the case until Friday when the court heard a post-mortem examination is to be held to establish how Mr Harris died.
He was in bed when the officers found him, but Ann Evans for the prosecution said no suicide note had been found.
Had the trial gone ahead, the prosecutor said five men now in their 30s and 40s would have come to court to tell a jury that they were sexually abused by Mr Harris when they were pupils at the school.
Mr Harris faced 30 charges alleging he had carried out serious sex offences and acts of indecency on the youngsters. The school has now closed.
The court heard Mr Harris had been due to plead not guilty to all the charges.
Mrs Evans said as a result of his death, the indictment against Mr Harris had no legal effect.
Judge Foster agreed and ordered the file on the case should be closed.