The National Institutes of Health last month published a startling analysis of how it allocates its funding: in 2010, HIV research received nearly $3.1 billion in funding, while a deadly lung disease that has more than six times the health toll in the United States got only $118 million.

Two diseases with a similar health burden, breast cancer and chronic liver disease, received wildly different levels of support: $763 million for the cancer best known for iconic pink ribbon awareness efforts, versus $284 million for a disease commonly caused by alcohol abuse. Autism receives more than five times the funding of eating disorders, but their impacts on health, measured in years of disability and premature death, are quite close.

The differences are an illustration of just how complex - and sometimes surprising - national decisions are about how to allocate research money. It might seem that research dollars should follow public health impact, with the diseases that cause the most harm attracting the most money. Overall, most diseases do follow that general pattern. But the outliers can be significant -- HIV currently gets 10 percent of the NIH budget -- and highlight just how complex and baffling this process can be, influenced by factors that range from the amount of scientific opportunity to make progress to the level of human suffering.

The overarching question of how we budget our federal research dollars has special currency right now, since the wildly popular bipartisan 21st Century Cures bill that passed the House last week calls for the biggest increase in NIH funding in more than a decade (aside from the one-time surge of money from the stimulus). Everyone seems to agree the NIH needs more money. But what should it be used for?

"There’s been a lot of attention on Capitol Hill about this," said Carrie Wolinetz, associate director for science policy at NIH. "It's been discussed in the context of 21st Century Cures. There's a lot of public attention."

This issue has arisen periodically over the years. Various research teams have crunched the numbers themselves. In 1999, in the midst of a period of storied growth for the NIH when the budget doubled over a five-year period, the issue came up repeatedly, with the Institute of Medicine calling for NIH to do a better job evaluating the disease burden and communicating to the public how funding choices are made.

Wolinetz said this is the first time that NIH has put out its own analysis of the breakdown of research funding versus burden of disease, a signal of transparency that many outside researchers applauded.

Claiborne Johnston, dean of the Dell Medical School in Austin, Tex., found in a 2011 PLoS ONE study that a third of the variation in how much money each disease area received could be explained by looking at the toll of human suffering. To quantify the burden of each disease, he tallied up years of life lost to the disease plus years of disability the disease caused. That measure is called disability adjusted life years, or DALYs for short.

Johnston said he's come to think that it's overly simple to assume that funding should be a mirror reflection of societal burden. The fact that HIV research receives  roughly 10 percent of the NIH budget, for example, may seem terribly out of whack with the toll the disease takes as treatments have been developed. But a compelling argument could also be made that investing more now to cure and eradicate HIV permanently would be helpful to society and patients. Others have argued that the HIV example also demonstrates the astonishing progress that can be made when a concerted, prolonged investment is made into a biomedical problem and could serve as a model for how to move forward against other diseases.

Still, looking at the disparities can be illuminating.

“The thing I found fascinating, and this still appears to be the case, is we tend to underfund things where we blame the victim,” Johnston said.

Take chronic obstructive pulmonary disease, also known as emphysema. It received $118 million in funding, but is the third leading cause of death in the U.S. The people who get that disease are overwhelmingly smokers. Perhaps since the solution seems clear and traditional -- stop smoking -- there isn't research done on new interventions, despite the toll the disease takes. Likewise afflictions like depression and liver disease from drinking, are part of a “societal cluster" that have been underfunded compared to the threat they represent, Johnston said.

A few years ago, the National Institute of Mental Health began to analyze the question. Thomas Insel, the director of the institute, said he found the analysis illuminating. It led to an increased focus on suicide and eating disorders.

"When we did it internally, it became really clear that an area that was really underfunded was suicide research," Insel said. "I just really didn’t realize that. I thought we had a lot more invested there. I should have known. I should have figured it out some other way, but it wasn’t until I saw the graph that I realize that was an area we needed to build."

Insel said that there are good reasons that overall funding should not track public health burden strictly. Rare diseases would be neglected, and the nature of science is that investment in one disease area can often have broader benefits. It's also important to remember that half the NIH budget is also spent on general scientific projects that can't be classified by disease and might yield insights or tools useful in many areas.

But William Young, president of Alliance for Headache Disorders Advocacy and a physician at Thomas Jefferson University who has studied the stigma associated with migraines, argues that the funding levels should track much more closely the burden. He believes advocacy discrepancies that trickle down to funding differences: diseases that haven't captured widespread public support, such as headaches, are often underfunded.

"If the purpose of NIH is to relieve the burden of disease, then studies should focus on where the disease burden actually is," Young said in an e-mail. "There is also the issue of fairness – people who have a disease that is unpopular have just as much right to benefit from research as those with a more popular disease. "