LAST week, the New York State Legislature struck a deal ensuring that charter schools in New York City would have access to space, either in already crowded public school buildings or in rented spaces largely paid for by the city. Over the next few years, charters are expected to serve an increasing proportion of city students — perhaps as much as 10 percent. Which brings up the question: Is there a point at which fostering charter schools undermines traditional public schools and the children they serve?

The experience of Harlem, where nearly a quarter of students are enrolled in charter schools, suggests that the answer is yes. High-quality charters can be very effective at improving test scores and graduation rates. However, they often serve fewer poorer students and children with special needs.

In Harlem, there is a marked disparity between the special-needs populations in charter and traditional public schools, according to the city education department’s annual progress reports. In East Harlem, data for the 2012-13 school year shows that most of the public open-enrollment elementary and middle schools have double, and several have triple, the proportion of special-needs kids of nearby charter schools. At most of these public schools, at least a quarter of students have Individualized Education Programs, or I.E.P.s, which are required for children who receive special-education services.

Students with I.E.P.s also tend to leave New York City charter schools at higher rates than their general-education classmates, according to a 2014 study by the city’s Independent Budget Office. Among special-needs students enrolled in charter schools in kindergarten in 2008, 27 percent had transferred to a traditional public school by third grade; the corresponding rate for general-education students was 17 percent.