George Rowland, a consultant gynaecologist, made his decision just minutes before Denise Bannister, from Wigan, was due to have an operation - after learning that she smoked 15 cigarettes a day.
Until now, such controversy has focused mainly on heart patients who have been told they can only have surgery on the condition that they give up smoking - for clinical reasons.
Miss Bannister's case is believed to be the first in which doctors have refused treatment for a condition unrelated to the effects of cigarettes.
She was due to have a simple operation on her fallopian tubes at Billinge Hospital, Wigan, last Friday. She had waited several months and was due to be a day-patient. She already has one child and lives with her partner.
A spokeswoman for Wigan and Leigh Health Services Trust, which runs the hospital, said: 'It was agreed with Miss Bannister earlier that she could have the treatment on the condition she gave up smoking. When it was discovered she was still smoking, she was discharged.'
Mr Rowland often advised all patients who were smokers to give up as it lessened their chance of conceiving and could harm an unborn child. She said the trust had no policy on whether smokers should get fertility treatment, but it 'thoroughly backed' the consultant's decision.
The British Medical Association said it was unethical to discriminate against a group of patients on anything other than medical grounds. 'When consultants inflict their own whims on patients, it is a very worrying departure,' a spokesman said.
Issue, formerly the National Fertility Association, said people who were infertile were already under a lot of stress. 'We would advise anyone who wants to have a baby not to smoke. But doctors should not make decisions based on people's lifestyles,' John Dickson, executive director, said.Reuse content