The risk rose fivefold in early pregnancy compared with women who conceived naturally, researchers found.
IVF is linked to more cases of pulmonary embolism, in which a blood clot causes a blockage in the main artery of the lung, and venous thromboembolism - blood clots which form elsewhere but can break off and become life threatening.
The researchers believe doctors should be aware of the danger, saying the number of cases remains small but blood clots on the lung are a leading cause of death in pregnant women, the 'Daily Mail' reported.
They suggest the reason may be a huge rise in oestrogen levels triggered by IVF drugs, with the effect diminishing later in pregnancy.
Hormonal drugs are widely used in IVF to stimulate the ovaries, allowing up to 15 eggs to mature and be removed from a woman's body at the same time.
In the latest study, researchers from the Karolinska Institute in Sweden compared the risk of both pulmonary embolism (PE) and venous thromboembolism (VTE) in almost 24,000 women having an IVF pregnancy and 117,000 women having a normal pregnancy.
Women were matched for age, with an average of 33.
The study found the proportion of IVF women diagnosed with VTE was 4.2 in 1,000 compared with 2.5 in 1,000 for those who had a natural pregnancy.
The proportional risk for those who had had IVF compared with those who had not was highest in the first three months of pregnancy: 1.5 in 1,000 compared with 0.3.
There was no difference in risk before pregnancy or during the year after delivery.
Researchers identified 19 women with potentially life-threatening artery blockages in the IVF group (a rate of 0.08 per cent) compared with 70 women (a rate of 0.05 per cent) having natural pregnancies.
The risk in the IVF women was increased during the whole pregnancy and particularly in the first trimester.
Absolute risks for pulmonary embolism were low however, with two to three additional cases per 10,000 IVF women, found the study.
Study leader Professor Peter Henriksson said it was not clear why IVF mothers were more at risk, but hormonal drugs were a plausible cause.
"During the IVF procedure hormonal drugs are given to stimulate the egg follicles to grow more eggs. This increases oestrogen levels in the body between ten and 100-fold and is likely to impact on the coagulation of the blood and increase blood clot formation," he said.
"It is highest during the first third of pregnancy, then eases off and the risk goes down to about the level of a normal pregnancy," he added.
