At the heart of the hysteria over vaping is what seems like a simple question: Is it safer than smoking?

Answering that question, however, is complicated. While e-cigarettes contain and produce fewer known cancer-causing toxins than cigarettes, that’s not the only factor at play. There are a host of unknowns about e-cigarettes, largely because long-term studies on their use have not yet been completed.

A new paper published in the American Journal of Preventive Medicine presents the findings of what’s thought to be the first longitudinal analysis of the association between vaping and lung disease. Researchers tracked e-cigarette users for three years, and found that they had a 1.3-times higher risk of developing respiratory disease than people who did not use any tobacco product. Meanwhile, cigarette smokers had a 2.5-times higher risk, and those who both smoked and vaped had a 3.3-times higher risk.

“If you’re going to do one or the other, in terms of these respiratory effects you’re probably better off with an e-cigarette,” says study co-author Dr. Stanton Glantz, a professor of medicine at the University of California, San Francisco and a leading researcher (and critic) of e-cigarettes. Even still, Glantz cautions that his prior research—some of which was later retracted—has found similar levels of cardiovascular risk associated with smoking and vaping; this was outside the scope of the new paper.

“This study actually does support the harm reduction potential of e-cigarettes,” says Andy Tan, an assistant professor of population sciences at Dana-Farber Cancer Institute who has studied e-cigarettes. “Yes, vaping is associated with about 29% to 31% higher odds of subsequent lung disease within two to three years than not vaping—but compare this with the 156% higher odds of using combustible tobacco than not smoking.”

For the purposes of the study, Glantz and his co-author combined four conditions—chronic obstructive pulmonary disease (COPD), chronic bronchitis, emphysema and asthma—into one respiratory disease umbrella. They used data provided by about 32,000 adults who responded to the U.S. National Institutes of Health’s Population Assessment of Tobacco and Health (PATH) study, which asks individuals about their tobacco-product use, general health and demographic profile.

When respondents first joined the PATH study, about 5,500 already had respiratory disease. About 12% of the total sample identified as former e-cigarette users, while 5.5% were current users. Meanwhile, 45% were former combustible tobacco users and 26% were current users.

The individuals were then asked to take follow-up PATH surveys one and two years later, reporting any changes to their tobacco use and health. About 1,100 people developed respiratory disease in the following years. The researchers found that both nicotine e-cigarette and combustible tobacco use were associated with a higher risk of developing respiratory disease, but vaping seemed to be less dangerous than smoking—and using either product alone was better than using both.

Glantz says that’s the most important finding from the paper, since about 60% of adult vapers also smoke, according to the U.S. Centers for Disease Control and Prevention’s latest estimate, and Glantz’ prior research has uncovered sizable cardiovascular risks associated with dual use. Research suggests some of the health risks associated with smoking and vaping are the same, but, due to their different formulations and delivery methods, many are different.

In Glantz’ study, for one, the link between vaping and developing lung disease was treated as distinct from the link between smoking and lung disease. It’s difficult to untangle how past and current habits contribute to a person’s disease risk—a former smoker who switches to vaping likely has a different risk profile than someone who went straight to vaping—but Glantz says their analysis accounted for those different scenarios. After running the raw data associated with current and former smoking and vaping, and mixtures of those scenarios, through their predictive model, the researchers found that they were almost completely distinct variables. What that means for a user, Glantz says, is dual use causes risks to multiply, rather than increase only modestly.

While the new study can’t prove cause and effect, only uncover patterns present among smokers and vapers, it’s among the most comprehensive analyses of e-cigarette use and respiratory disease yet. Past studies have shown links between vaping and some of the respiratory diseases mentioned in the paper, but they have mainly looked at snapshots in time, rather than changes over time.

Glantz says three years isn’t a terribly long time to follow vapers—especially since many people who entered the study as smokers had likely started that habit earlier, allowing risks to accrue. A cigarette user could have smoked for decades before entering the study, but since e-cigarettes had only been on the U.S. market for about six years when the study began in 2013, it’s unlikely that most people in the sample had vaped for a lengthy period of time. That means long-term risks may be only beginning to emerge.

“Based on what we know about the biological effects of e-cigarettes, my guess is that if we followed these people for 20 years, the e-cigarette effect would be similar [to the risks associated with smoking,]” Glantz says.

Glantz’ position is controversial, since other studies have estimated that wide-scale switches from smoking to vaping could save millions of lives by reducing the burden of smoking-related diseases. (Importantly, Glantz’ analysis also did not include risks of lung cancer, one of the leading killers associated with smoking.) Regardless, the research adds fuel to the already contentious vaping debate.

This story has been updated to reflect the retraction of Glantz’ study on vaping and cardiovascular risk.

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Write to Jamie Ducharme at jamie.ducharme@time.com.