Earlier this year, watchdog Ofsted said it found evidence of homophobic and racist bullying at Grindon Hall, a Christian school in Sunderland. This prompted Ofsted to put the school into special measures.
Grindon Hall formally complained to Ofsted about the inspection, because inspectors asked pupils what lesbians "did".
The head teacher of Grindon Hall, Chris Gray, says the Ofsted inspection was "negative and hostile at every stage" and it was like the "data collected had to fit a predetermined outcome".
Ofsted also said it found evidence of bad behaviour, prejudice towards non-Christians and bullying at Durham Free School, a Christian school in north-east England.
The authority in charge of funding schools also said it had "serious concerns" about the way Durham Free School was managing its money.
This prompted the Department for Education to withdraw funding for Durham Free School, effectively closing it. Durham Free School has said it's contesting the decision.
Recently, MPs questioned Sir Wilshaw after they said they received several letters complaining their Christian schools were being unfairly targeted. In response, he categorically denied Ofsted was prejudiced against Christian schools.
Sir Michael Wilshaw said Ofsted inspectors are "well trained, vastly experienced professionals who absolutely understand the need to behave with sensitivity and integrity.
"This is particularly important when they are following up serious allegations of prejudice-based bullying and derogatory name-calling.
"Inspectors had to couch questions using age-appropriate language that the children would understand... to find out what was happening.
He also denied the claim that he was anti-faith schools. He said: "As a former headteacher of a Catholic secondary school, the charge that I am presiding over some sort of state-sponsored, anti-faith school "witch-hunt" would be laughable - were it not so serious.
"I have long been a staunch supporter and proponent of faith schools in this country, believing that they are a valuable and enduring feature of our education landscape.
"Let me offer this unequivocal reassurance - the vast majority of faith schools have nothing to fear either from Ofsted or from the recent guidance issued by the Department for Education on promoting British values as part of the curriculum."
Durham Free School parent, Billy Lau:
