Not long ago, I asked a colleague for advice on a patient. He offered up a couple of treatment options, then stopped to show me a new medical app on his electronic tablet. With a few swipes of his finger, he summoned a compilation of research articles, synopses and even entire textbooks that, printed and bound, would have filled shelves in a library.

"But do you know what the best part is?" he asked with a twinkle in his eye. I thought of the exhaustive reference material and the seemingly endless scroll of diagnoses that were all so easy to access on the small screen balanced on his knees.

"The best part is that none of this is sponsored by Pharma!" he said with a broad smile. "There's no bias."

My colleague is not the only doctor who feels that way, according to a recent study published in The New England Journal of Medicine.

For years, most doctors have had a predictable, if not close, relationship with the pharmaceutical industry. Companies handed out office tchotchkes, paid for staff lunches and distributed drug samples for patients. More significantly, drug companies were important sources of biomedical research money, particularly during periods when federal support wavered. It was understood that the companies providing funding would leave the researchers alone to design and conduct the study, analyze the data and write up the results.

That understanding began to fray about a decade ago when doctors, and patients, began to realize that drug companies were becoming too involved with the research they were supporting. For example, one major pharmaceutical firm manipulated data and underestimated the risk of heart attacks, strokes and deaths in a large study of a drug for arthritis. The drug was eventually withdrawn from the market, but not before 80 million patients had used it, with annual sales topping $2.5 billion.

The case highlighted the dangers of industry sponsorship of research into new drugs, and the public became eager to expose any potential conflict of interest, particularly for doctors. Within a few years, a new standard of transparency in medicine emerged. Brightly labeled drug company pens became an embarrassment; lunches on the drug company tab and sponsored conferences turned suspect; and editors at numerous medical journals published lengthy screeds detailing their disclosure requirements.

The new skepticism and transparency were no doubt good for patients and doctors, but this recent study reveals that in our zeal to single out the pharmaceutical industry's biases, we may have become blind to our own.

The researchers created several hypothetical drug studies, then asked a group of practicing physicians to rate the "studies" and the likelihood they would prescribe the new "drug." The researchers purposefully varied the quality of the studies and the disclosures - some of the made-up studies disclosed that they had received pharmaceutical company funding, others said they'd received support from the National Institutes of Health, and the rest listed no funding disclosures at all.

Most of the doctors were able to assess the quality of the research pretty accurately. After reading the less rigorous studies, the ones that weren't designed, conducted or analyzed well, the doctors were hesitant to prescribe the new drugs under study; seeing the more rigorous studies, they were more willing to do so.

But the researchers also found that the doctors were also unduly swayed by any mention of industry funding. Regardless of the quality, if a study was supported by a pharmaceutical company, doctors were less willing to consider prescribing the studied drug and less likely to assess the quality of the research with accuracy.

"Some amount of skepticism is warranted," said Dr. Aaron S. Kesselheim, lead author of the study and an assistant professor of medicine in the division of pharmacoepidemiology and pharmacoeconomics at the Brigham and Women's Hospital in Boston. "But ultimately it should be the quality of the study and the impact of the results that determine your confidence about using a new drug, not who was funding it."

Being overly skeptical has serious implications for patient care. The pharmaceutical industry, along with medical device and biotechnology firms, continues to finance a majority of current research. In 2007, for example, industry was responsible for nearly 60 percent of the more than $100 billion spent on research. Much industry-supported research focuses on the side effects of new drugs. By writing off such research, doctors risk overlooking findings that may have important treatment implications for their patients, like a new cholesterol-lowering drug that is found to have less of an effect on energy and blood sugar levels than other similar medications.

Dr. Kesselheim and his collaborators believe what is needed in biomedical research is even greater transparency. Such openness would include more independent third-party statistical reviews to ensure that data is not being manipulated or misleading and wider use of public Web sites like ClinicalTrials.gov, regardless of the source of funding.

ClinicalTrials.gov lists study details like objectives, design and data gathered, providing doctors and patients alike with a way to confirm that no data is being selectively reported or distorted. But participation on the site is voluntary, and pharmaceutical, medical device and biomedical companies are often hesitant to share what they consider proprietary data, choosing instead to list only selective details, or no information at all.

Until full transparency is achieved and such details are available to all on the Web or for independent statistical reviews, Dr. Kesselheim and his collaborators suggest that both doctors and patients remain alert to potential biases - Big Pharma's, and also their own.

"Excessive skepticism," Dr. Kesselheim observed, "is as much a bad thing as naïveté."