“There were days I considered shutting the garage door and letting the car run until I was dead,” says Colorado mom Erin Griffin, of the time nine years ago when she learned that both her boys—not just her firstborn—suffered from autism. Brendan, her angular, dark-haired older child, was diagnosed in 1996 at age 4. Kyle, her round-faced, hazel-eyed younger son, was diagnosed in 1998 at age 2½.

But Kyle and Brendan’s story does not have a tragic ending. After interventions that included occupational and speech therapy, as well as dietary change and nutritional supplements, both boys improved significantly. Their tale of slow, steady recovery reflects the changing landscape of autism today. The condition, traditionally seen as genetic and originating in the brain, is starting to be viewed in a broader and very different light, as a possible immune and neuroinflammatory disorder. As a result, autism is beginning to look like a condition that can, in some and perhaps many cases, be successfully treated.

That is astonishing news about a disorder that usually makes headlines because it seems to be growing rapidly more widespread. In the United States, the diagnosis of autism spectrum disorders has increased about tenfold over the past two decades, and a 2003 report by the Centers for Disease Control suggests that as many as one in every 166 children is now on the autism spectrum, while another one in six suffers from a neurodevelopmental delay. This explosion of cases has raised countless questions: Is the increase real, is it the result of increased awareness and expanding diagnostic categories, is it due to environmental changes, or all of the above? There may be no single answer. But the public concern about autism has caught the ear of federal lawmakers. The Combating Autism Act, approved last December, authorized nearly $1 billion over the next four years for autism-related research and intervention.

Meanwhile, on the sidelines of that confusing discussion, a disparate group—immunologists, naturopaths, neuroscientists, and toxicologists—is turning up clues that are yielding novel strategies to help autistic patients. New studies are examining contributing factors ranging from vaccine reactions to atypical growth in the placenta, abnormal tissue in the gut, inflamed tissue in the brain, food allergies, and disturbed brain wave synchrony. Some clinicians are using genetic test results to recommend unconventional nutritional therapies, and others employ drugs to fight viruses and quell inflammation.

Above all, there is a new emphasis on the interaction between vulnerable genes and environmental triggers, along with a growing sense that low-dose, multiple toxic and infectious exposures may be a major contributing factor to autism and its related disorders. A vivid analogy is that genes load the gun, but environment pulls the trigger. “Like cancer, autism is a very complex disease,” says Craig Newschaffer, chairman of Epidemiology and Biostatistics at the Drexel University School of Public Health, “and it’s exciting to start asking questions about the interaction between genes and environment. There’s really a very rich array of potential exposure variables.”

In one way, the field seems like a free-for-all, staggeringly disordered because it is littered with so many possibilities. But one can distill a few revolutionary insights. First, autism may not be rigidly determined but instead may be related to common gene variants, called polymorphisms, that may be derailed by environmental triggers. Second, affected genes may disturb fundamental pathways in the body and lead to chronic inflammation across the brain, immune system, and digestive system. Third, inflammation is treatable.

“I can’t think of it as a coincidence anymore that so many autistic kids have a history of allergies, eczema, or chronic diarrhea.”

“In spite of so many years of assumptions that a brain disorder like this is not treatable, we’re helping kids get better. So it can’t just be genetic, prenatal, hardwired, and hopeless,” says Harvard pediatric neurologist Martha Herbert, author of a 14,000-word paper in the journal Clinical Neuropsychiatry that reconceptualizes the universe of autism, pulling the brain down from its privileged perch as an organ isolated from the rest of the body. Herbert is well suited to this task, a synthetic thinker who wrote her dissertation on the developmental psychologist Jean Piaget and who then went to medical school late, in her early thirties.

“I no longer see autism as a disorder of the brain but as a disorder that affects the brain,” Herbert says. “It also affects the immune system and the gut. One very striking piece of evidence many of us have noticed is that when autistic children go in for certain diagnostic tests and are told not to eat or drink anything ahead of time, parents often report their child’s symptoms improve—until they start eating again after the procedure. If symptoms can improve in such a short time frame simply by avoiding exposure to foods, then we’re looking at some kind of chemically driven ‘software’—perhaps immune system signals—that can change fast. This means that at least some of autism probably comes from a kind of metabolic encephalopathy—a systemwide process that affects the brain, just like cirrhosis of the liver affects the brain.”

In 1943 Johns Hopkins University psychiatrist Leo Kanner first described autism as a now-famous collection of symptoms: poor social engagement, limited verbal and nonverbal communication, and repetitive behaviors. Back then, autism was considered rare; Kanner first reported on just 11 patients, and Johns Hopkins still has records of about 150 patients he examined in total. Even within this small group of patients, other, less visible symptoms were evident. In his 1943 paper, “Autistic Disturbances of Affective Contact,” Kanner noted immune and digestive problems but did not include them in the diagnosis. One reads with a shiver sentences lifted out of various case histories: “large and ragged tonsils . . . she was tube-fed five times daily . . . he vomited all food from birth through the third month . . . he suffered from repeated colds and otitis media. . . .”