By Chris Seper

It’s hard to gauge the impact of The New York Times’ critique of WebMD. Is it just one columnist’s opinion? Or is it a signal that standards for online health advice are going to change?

Times columnist Virginia Heffernan cracked WebMD as “synonymous with Big Pharma Shilling” and the ultimate place for “hypochondria time suck.”

The commercialized nature of WebMD, Heffernan said, can’t hold a candle to the likes of MayoClinic.com, which takes a more straight-forward, calm and clinical approach backed up by the reputation of Mayo itself.

Mayo’s storied past as the country’s premier research hospital, in Rochester, Minn., and its storied present as one of Fortune’s ’100 Best Companies to Work For’ surface in the integrity of the site itself, which — though not ad-free — is spare and neatly organized, with the measured, learned voice of the best doctors. The byline for most entries is ’Mayo Clinic staff.’ The integrity of the whole institution is on the line with this site, and the Mayo Clinic has every motivation to keep its information authoritative and up to date.

Mayo’s response to the piece is as staid as Heffernan’s description of its site. “The general consensus at Mayo Clinic regarding the New York Times article from the weekend is that we’re pleased to be recognized for our quality and integrity, and as a credible source for health information online,” Mayo spokeswoman Ginger Polumbo said Monday.

But health systems, which were late dispensing online health information and are now trying to catch up, have to be rubbing their hands. The rule has typically been that content vetted by physicians and other experts meets the standard for top-tier health information (and WebMD follows this rule). And there are so many atrocious health sites offering dangerous and poor medical advice (anorexia, anyone?) that few would think to knock WebMD’s approach.

But Heffernan suggests a higher standard: that advice directly from reputable health systems beats third-party reporting coupled with a review, particularly when there is a greater financial motive behind the latter approach.

News flash: WebMD is a business that wants to make money. Its advertising is clear but can be too subtle. Banner ads are obvious and clearly labeled with small type, though the WebMD-based advertiser pages are easy to mistake for WebMD content.

Heffernan dislikes the amount of pharmaceutical advertising on WebMD and the fact advertising related to the affliction is in and around related content. I think that’s a bogus assertion that runs counter to the online targeting that makes the Web so great (and, as John Sharp points out, this happens at MayoClinic.com as well). Both WebMD and Mayo have fair and transparent advertising policies, though the real issue is how the sites practice what they preach. In look, Mayo has less of a commercial feel.

Though I wonder if that’s all by design. Heffernan underestimates the financial motivation behind any health site run by any institution. Seeking health information is the third most popular activity on the Web behind checking e-mail and using a search engine, according to a new study from Pew Research Center.

Mayo has been making money from its health content by creating personalized portals for private organizations or licensing its health articles to media organizations. In late 2009, it connected with the Everyday Health Network to increase online advertising revenue.

Then there’s the bigger opportunity: using a health site for national and global brand building to attract a number patients who will travel for good healthcare.

MayoClinic.com’s Web traffic enjoyed a surge over the past several years as it jumped ahead of other health information providers. But its numbers and WebMD’s have stabilized, according to the likes of Compete.com and Quantcast. MayoClinic.com has about one-third of WebMD’s traffic, according to those measurement tools.

That flattening of numbers could be due in part to the increase of hospital-made WebMD-like sites, which I believe will be essential for any major health system as part of their marketing efforts.

But amid a glut of health content, good and bad, the idea that direct-for-the-health system content is the best would be a major change. I used to hear people argue the opposite: that there are pluses to having outlets besides hospitals, which have the potential conflict around driving referrals and preference toward certain treatments and research, produce third-party advice (a practice formerly known as journalism).

But increasingly I hear the opinion echoed by the journalist Heffernan. And such a change would mean that health systems, which lost some of its influence for health information before the Internet revolution, would suddenly regain mindshare they lost to the Web and the WebMD’s of the world.

And you can’t put a price on that.