Parents of children admitted to the STEM citywide gifted program at P.S. 85 attend an open house Wednesday.

Every morning, Tim Smith and his nine-year-old son leave their Bronx home at 7:30 a.m., catch a MetroNorth train to 125th Street and then board the M60 bus into Queens — all so the third-grader can attend P.S. 85 in Astoria, home to one of New York City’s handful of citywide gifted-and-talented programs.

Even so, they brace themselves for an even more difficult journey ahead: Finding a middle school.

In 2009, when P.S. 85′s program opened as part of an effort to expand gifted education, the Department of Education pledged “to identify nearby middle schools where students in these programs can continue after fifth grade.” But last month, responding to parents’ pleas to make good on the promise, the department informed them that P.S. 85 cannot handle expansion into a middle school because it is already “operating close to 100 percent capacity.” It said students in the gifted program — called the STEM Academy (it stands for Science, Technology, Enrichment and Math) — must go to middle school elsewhere.

STEM is the only citywide gifted-and-talented elementary school program that ends with fifth grade. (It is the only citywide gifted program housed within another school.) Three of the four other citywide programs — Manhattan’s Anderson School and TAG Young Scholars, as well as the Brooklyn School of Inquiry — continue through eighth grade, and Manhattan’s NEST+M carries students through the end of high school.

“The school was meant to be a peer for the other citywide gifted programs, and admission to a middle school program was supposed to be seamless,” said Smith.

STEM parents charge that their program has been neglected because of a shift in priorities at the Department of Education.

Under former schools chancellor Joel Klein, gifted education expanded at a rapid clip, with an eye on keeping young families in the city and choosing public schools. In 2009, gifted schools opened in Brooklyn and Queens, including at P.S. 85. Even more were promised on the way.

“We’re going to open citywide programs in other parts of the city in the coming years as we continue to increase our outreach about the admissions process and identify as many of our City’s gifted students as possible,” wrote Klein in a March 2009 press release.

Now, the office of gifted education, formerly run by Anna Commitante, no longer exists, and the link to it on the Department of Education’s website connects only to information about admission to gifted programs. The Department did not return repeated calls and emails for comment.

Parents recall that the office was dismantled amid transitions from Klein to former schools chancellor Cathie Black in favor of a more inclusive approach to education. They say that children in gifted programs are losing out as a result.

The office was “for people who were not just figuring out enrollment and doing testing, which is all they do now,” said parent Michelle Noris, who has a child at P.S. 85. “There were people who were working on curriculums and creating programs. … Focus away from gifted and talented programs is, I think, part of an overall approach to heterogeneous classes.”

Other parents note that while department officials have promised to open 50 new middle schools over the next two years, they have not designated any as a citywide gifted program.

Parents at P.S. 85 say the absence of a middle school diminishes the appeal of their program. They say all that they are looking for is a guarantee that the kids will have a place to go for grades six through eight. The Community Education Council for District 30 this week passed a resolution supporting their effort.

“STEM is the forgotten citywide program because it’s not Brooklyn or Manhattan. We are the only one that’s not K-through-8, we sort of feel like the forgotten citywide program,” said Michal Melamed, whose first-grade son commutes to P.S. 85 from Manhattan. “We want equity with the other citywide programs.”

The citywide programs require the highest scores for admission: To enter a program such as P.S. 85’s, children must have scored in the 97th percentile or above on two screening tests. Last week, parents found out whether their children had made the cut for this year — and more than 2,600 incoming kindergarteners scored high enough to qualify for admission to citywide programs. But last year, those programs had only about 300 seats, making admission about as likely as getting into Harvard University.

Pressed about the shortage of seats in gifted programs, Chancellor Dennis Walcott said this week that the department was looking for ways to accommodate more of the children whose scores qualify them for admission but that more seats would likely not be added to citywide programs.

For now, current STEM parents must decide whether to try to procure a spot in the other citywide programs (a very long shot) or seek alternatives for middle school. The program’s oldest students are in third grade this year.

“There is a fair amount of scientific literature that suggests that it’s really hard for kids to switch school in middle school,” said Melamed. “Data suggests that having a K-through-8 model is how most of our schools should run.”

Mehrunnisa Wani is a student at Columbia University’s School of Journalism. A version of this story originally appeared on New York World, a project of the journalism school.