Pediatricians are not supposed to have favorite patients, but I will admit that every time I see one 5-year-old boy — call him Amir — my day brightens. Amir is charming and precocious, and his mother, whom I’ll call Fatima, is attentive and loving. They are a delight.

Amir has significant intestinal issues that preclude him from eating most processed foods. Because he and his mother are homeless, they have been placed by the state in a motel room where they have only a microwave for a kitchen. Motels are the Commonwealth’s answer to the severe shortage of beds in homeless shelters — on the day after Thanksgiving, there were nine open beds in state shelters and 2,159 families in motel rooms.

Overall, more than 4,100 families are in shelters and motels in the state, an all-time high — and a number that could rise through next summer.

The motels are woefully inadequate for keeping children healthy, even children without Amir’s problems. There is often no place to play safely, no way to cook nutritious food, and a lack of nearby social supports. So, while homeless families technically have a roof over their heads, their bodies and brains are still threatened.

At our last visit, Fatima told me that she had devised a way to prepare food Amir could eat using a rice cooker — he could now have freshly made stews, she told me with relief.

“But what are you eating?” I asked.

“Oh, well.” She looked down. “I needed to lose weight anyway.”

Fatima, who recently lost her job as a housekeeper, has been eating mostly cheap canned soups, full of salt and preservatives. She can’t afford fresh food for both of them. I can send them to our food pantry, but that seems futile, because I can’t give her the means to cook or store what she would get there.

I work at Boston Medical Center, where the pediatric emergency room sees 28,000 children a year. A survey of 6,000 Boston-area families by the pediatric research center Children’s HealthWatch estimated that more than half of the children younger than 4 were housing insecure, moving frequently or otherwise living in unsafe or inappropriate housing. Such children are more likely than their housing-secure peers to get hospitalized, be hungry, and have developmental delays. As Dr. Megan Sandel, a BMC pediatrician and longtime housing advocate, often says, housing is a vaccine; it protects our children from hunger, disease, and violence, just as a shot protects them from measles.

Alarmingly, being housing insecure in Massachusetts does not necessarily qualify a family for shelter. In 2012, the eligibility requirements were sharply restricted, and as of April 2013, up to 75 percent of applicants were being denied placement, sometimes because they couldn’t prove they had slept somewhere unfit for human habitation, like a car or a bus station.

When BMC social worker Nikki Hinckley talks about these families, her voice is tense. She talks about a child with sickle cell disease, a condition where cold weather can bring on intense pain, strokes, and life-threatening lung problems. The family was sleeping in a cold church basement, which disqualified them for shelter but landed the child in the hospital. She talks about autistic children living in crowded conditions, causing them severe emotional distress, and families who come to the ER over and over, trying to find a way to get housed. “It’s just awful, sitting in front of families day after day saying we have nothing to offer them,” she says.

HomeBASE, a temporary housing subsidy program put in place in 2011, was supposed to be an answer to the combined crisis of housing insecurity and unsuitable motels. It was originally intended to provide three years of assistance to homeless families, supplementing their income so that they could afford apartments, get on their feet, and ideally start paying their own rent. It expired this summer, after the Legislature voted to shorten the program by a year.

More than half of the state’s approximately 5,000 HomeBASE families will have lost their subsidies by the end of this month, according to the Metropolitan Boston Housing Partnership, or MBHP. The rest will lose them by the end of July. Although new stipends from the state have helped keep many of those families off the street so far, the funds top out at $8,000, which doesn’t go far around here. “All bets are off once that assistance is gone,” says MBHP executive director Chris Norris.

According to a May 2013 report from MBHP, which administers the HomeBASE program in the Boston area, program families had an average monthly income of $845, with an average monthly housing cost of $1,283. In one of the nation’s most expensive housing markets, it was unrealistic to expect that these families could get to the point where they could afford their rent without the support. Ironically, those in motels end up costing the state roughly $2,400 a month, significantly more than paying their full rent would be.

Norris, Sandel, and others believe the answer is permanent income-adjusted housing subsidies. These would require a significant initial investment, and we would need to maintain a shelter safety net as long as it’s needed.

But we know that temporary subsidies don’t work and that the motel system is unhealthy and expensive — the rooms now cost the state $46 million a year. And data from a program for homeless adults indicate that subsidies would likely be cheaper than health care and other services currently used by housing-insecure families.

Permanent subsidies introduced without further restricting access to the shelter system would be a real, cost-effective investment in lives like Amir’s, and our legislators need to know that’s an investment we want them to make.

Dr. Alexandra Coria is a pediatric resident at Boston Medical Center and Boston Children’s Hospital. Send comments to magazine@globe.com.

Link to article can be found here: http://www.bostonglobe.com/magazine/2013/12/22/how-massachusetts-failing-homeless-families/9UZIwZDStVfaDvLV9fnPsL/story.html