Annie, my friend John's kid sister, got sick when she was 11. I wasn't much older so I didn't know how serious it was when John said her disease was called lupus. I didn't realize her own cells were attacking her, sometimes going after her kidneys, other times her lungs. I did know, because her brother told me, that her face got really swollen because she had to take lots of pills called steroids, which had side effects that meant she could get very sick from flus or colds that he and I shrugged off. At times Annie missed long periods of school. At times she hurt badly. As she grew, she worked in children's theater, which she adored, and in local politics. Annie never got past lupus, though. She died at age 49.

Too many stories end this way. Lupus is an autoimmune disease, in which the body's guardian immune system turns traitor and tries to destroy the organs it is meant to protect. There are about 80 of these disorders—some estimates are higher—and in the U.S., almost 25 million people suffer from them, according to the National Institutes of Health. The number appears to be rising. The illnesses range from the familiar, such as type 1 diabetes and lupus, to the obscure, such as Takayasu's arteritis (in which large blood vessels become dangerously inflamed).

This special report highlights new discoveries about these ailments, too often understudied given their terrible toll. Fresh ideas are emerging about the ways such disorders get started, ideas that run counter to a century of medical dogma. And researchers now have theories that could explain the awful gender imbalance in autoimmune disease—nearly 80 percent of patients are women. These advances are leading to more refined treatments, based on a more nuanced understanding of our immune systems. Progress is still slow, but the changes carry with them hopes of overwriting a past filled with ineffective therapies or drugs that could be worse than the diseases themselves.

How I Was Betrayed from Within

One patient recounts her journey through a world of disabling symptoms, ineffective treatments and dismissive doctors

The Terrible Toll of 76 Autoimmune Diseases

This list shows how common each disorder is, which body parts are stricken, and the illnesses’ tendency to afflict women

In Autoimmune Disease, Organs May Lure the Immune System into an Attack

New evidence indicates that target cells may play a role in their own destruction

Why Nearly 80 Percent of Autoimmune Sufferers Are Female

The effects of sex hormones, X chromosomes and different gut microbes may be parts of the answer

Targeted Treatments for Autoimmune Disease Make Progress

By aiming at specific genes or cells, researchers can boost effectiveness and reduce side effects