US researchers found the type of fat, not the total amount, was a risk factor in developing the condition.
Previous studies had suggested a link between omega-3 intake and improvement in endometriosis symptoms.
Researchers at Brigham and Women's Hospital, Boston, assessed the diets of 70,709 women over 12 years using questionnaire data.
A total of 1,199 cases of endometriosis were reported. Women who ate the highest amount of long-chain omega-3 fatty acids were 22 per cent less likely to be diagnosed with endometriosis than those who ate the least.
However, the highest trans fat intake was associated with a 48 per cent increased risk, compared with those who ate the least.
Lead author Stacey Missmer said: 'Millions of women suffer from endometriosis. Many women have been searching for something they can do for themselves, or their daughters, to reduce the risk of developing the disease. These findings suggest that dietary changes may be something they can do.'