The risk was most pronounced in women over 60, who saw rates of arterial and heart diseases rise 32 per cent relative to women who did not take antibiotics during the eight year study period.
"Antibiotic use is the most critical factor in altering the balance of microorganisms in the gut," senior author of the study Professor Lu Qi, director of the university's Obesity Research Centre, and a professor at Harvard said.
"Previous studies have shown a link between alterations in the microbiotic environment of the gut and inflammation and narrowing of the blood vessels, stroke and heart disease."
The study, published in the European Heart Journal, used participants in a long running US study including 36,500 women were monitored over nearly eight years.
Over this period, 1,056 participants developed cardiovascular disease, but the absolute risk of issues remained low.
Among women 60 plus there were six heart attacks or strokes per 1,000 women, compared to three per thousand in women the same age who didn't take antibiotics. this increase remained pronounced even after controlling for other health risks or factors that might explain the rise.
Women in middle age had a smaller, but still pronounced increased risk of around 28 per cent, but there were no effects found in women aged 39 or younger.
"As these women grew older, they were more likely to need more antibiotics, and sometimes for longer periods of time, which suggests a cumulative effect may be the reason for the stronger link in older age between antibiotic use and cardiovascular disease," said Dr Yoriko Heianza, another of the authors.
Antibiotics alter the balance of the gut ecosystem, destroying beneficial bacteria and increasing the prevalence of viruses, harmful bugs and infectious fungal organisms such as Candida.
Women in the study most commonly took antibiotics for lung infections, urinary tract infections, and dental problems.
Prof Qi added: "Our study suggests that antibiotics should be used only when they are absolutely needed.
"Considering the potentially cumulative adverse effects, the shorter time of antibiotic use the better."
Additional reporting by PA