Birmingham, England - Dr David Drew, 64, told an employment tribunal that he was made to feel like a "religious maniac" after sending out the prayer by St Ignatius Loyola, founder of the Jesuits, to motivate his department.
But Employment Judge David Kearsley ruled that if complaints were made about Muslim or Hindu doctors who had quoted from holy texts, they too would be asked to refrain from such behaviour.
Similarly, if an atheist consultant caused unease by trying to educate his colleagues about "the works of Richard Dawkins or Christopher Hitchens", he or she would be treated in the same way, the judge said.
Dr Drew, a former clinical director, said the prayer was intended to offer inspiration in his "frail and imperfect efforts" to serve his patients and the department.
The Birmingham tribunal heard that he had also sent emails to colleagues in which he quoted from poems and from the Bible. One said he found it "strange" and another felt they were "bizarre and inappropriate".
The doctor said problems began when he voiced concerns about practices at Walsall Manor Hospital, Birmingham, in 2008.
He was first suspended in April 2009 following a complaint by a senior nurse that he was undermining her, but which was subsequently dismissed.
Following an independent review of his conduct, a report concluded that Dr Drew's religious language was inappropriate in a professional business setting.
He was told that such communication was unacceptable and that his religious beliefs should be kept to himself.
The report also criticised Dr Drew for sending a text message to a colleague, Rob Hodgkins, reading "Have a peaceful Christmas" which was perceived as an "aggressive and unwelcome intrusion" into his private time.
Dr Drew, a father of four who lives with his wife Janet, 61, in Sutton Coldfield, West Mids, refused to adhere to the report's recommendations and was dismissed for "gross misconduct and insubordination" three days before Christmas in 2010. He lost an appeal last April.
During an eight-day employment tribunal, Sue James, chief executive of Derby's hospitals said that Dr Drew produced a "toxic environment" at the hospital by constantly raising complaints against his co-workers and described the religious references as "highly marginal".
Judge Kearsley concluded that there was "no evidence" that members of the hospital board "were influenced, even subconsciously, by a prejudice against Christians when compared to persons of others faiths or no faith at all".
The hearing heard that on occasion, Dr Drew used the phrase "I am a Christian, therefore.." whilst at work.
But the judge said: "There is no need for such assertions in professional communication nor was there a need to make religious references if they are considered inappropriate and if they hinder proper communication."
Dr Drew said last night that the case would have major implications for any workplace.
"This means that you cannot be yourself in the workplace, you cannot say 'I am a Christian'," he said.
"Other people who have got other religions won't be allowed to either but of course what religion other people are because it is more visible.
"For example we would be in meetings when one or two of my colleagues who are Muslims would go across into a corner to pray.
"The Muslim doctors have been more supportive of me than any other groups and I has a very warm working relationship with them."
Dr Drew, who describes himself a committed "Christian with Questions" brought the case independently. His lawyers are now considering whether to appeal.
Andrea Williams, director of the Christian Legal Centre, which brought a string of other court cases involving claims of discrimination against Christians at work, said: "This is like the shutting down of identity. This approach to Christians is like forcing them to deny their identity – being Christian isn't something which you take off when you go to work.
"To say that it is not appropriate to say that you are a Christian at work is to totally misunderstand our history, our heritage, freedom under the law, freedom of religion, it is deeply illiberal, it is wrong."
But Stephen Evans, campaigns manager at the National Secular Society, said the claims of religious discrimination were unfounded.
“The most disturbing aspect of Dr Drew's case is that it is precisely the kind of nonsense that senior politicians including the Prime Minister are referring to when they claim Christianity is being marginalised in the UK and call for a Christian ‘fightback’ against secularism,” he said.
“Yet again we find that when claims of discrimination against Christians in the workplace are properly scrutinised, they fall flat on their face."