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Thousands of Scots children are born suffering internal organ damage, facial malformation or have learning difficulties as a result of their mothers drinking too much during pregnancy, according to a report.

Women who binge drink in the first three months of pregnancy can cause Foetal Alcohol Syndrome (FAS) which manifests in a malformed face and potentially fatal damage to the brain and organs. The less obvious Feotal Alcohol Spectrum Disorder (FASD), caused by drinking in the later stages of pregnancy, results in learning and concentration difficulties.

A study by Children in Scotland, which has more than 450 members including children's charities and community groups, showed that a "conservative estimate" of 900 children were suffering from the syndrome, and many thousands more from the disorder.

Dr Jonathan Sher, who compiled the report, which has been sent to both the UK and Scottish parliaments, warned that too much emphasis has been placed on the cost of adults misusing alcohol and too little on the impact on unborn children.

Dr Brian Keighley, chairman of the BMA in Scotland, said: "We need to raise awareness of the emerging evidence on FASD among healthcare professionals so that children are diagnosed quickly and get the help they need. The lack of awareness and research in the UK on this subject, together with the complexity of the syndrome itself is leading to delays in diagnosis and referral.

"Healthcare professionals also need to get the message across to expectant mothers that consuming alcohol can cause irreversible harm to their unborn child. It's about giving people the right information so that they can act responsibly - and save children from completely preventable life-long disabilities."

Dr Richard Simpson, Scottish Labour Health spokesman, said: "The conclusions of this report are shocking. Children's charities are absolutely right to highlight the impact of alcohol abuse on unborn children and raise awareness about the dangers of alcohol consumption in pregnancy.

"I believe that expectant mothers should be given much clearer advice, but we also need to deal with problem drinking at an earlier stage. The truth is that too many young women, and young men, are drinking excessively."

In 2007 the BMA called for further urgent research on FASD, especially the relationship between different levels of prenatal exposure and the range of conditions associated with the disorder.

It said the UK health departments should implement guidance and training programmes for healthcare professionals on the prevention, diagnosis and management of the condition and women who were pregnant, or considering pregnancy, should be advised not to consume any alcohol.