Substitute schools were preselected for the public school samples by sorting the school frame file according to the actual order used in the sampling process (the implicit stratification), except that the last ordering was done by estimated grade enrollment instead of median income. Each sampled school had each of its nearest neighbors within the same sampling stratum on the school frame file identified as a potential substitute. The last sort ordering was by grade enrollment so that the nearest neighbors had grade enrollment values very close to that of the sampled school. This was done to facilitate the selection of about the same number of students within the substitute as would have been selected from the original sampled school.
Schools were disqualified as potential substitutes if they were already selected in the public school sample or assigned as a substitute for another public school (earlier in the sort ordering). Schools assigned as substitutes for twelfth-grade schools were disqualified as potential substitutes for fourth- and eighth-grade schools, and schools assigned as substitutes for eighth-grade schools were disqualified as potential substitutes for fourth-grade schools.
Schools were also disqualified as potential substitutes at grades 4, 8, and 12 if they had been selected for the original Progress in International Reading Literacy Study (PIRLS) sample. Substitute schools in the PIRLS sample were disqualified as potential (NAEP) substitutes for grade 4, but allowed as potential (NAEP) substitutes at grades 8 and 12. Finally, schools selected for the NAEP-related Sensitivity to Instruction (STI) Study were disqualified as potential substitutes at grade 8, but allowed at grades 4 and 12. See the NAEP 2006 Sample Design for more information about PIRLS and STI.
If both nearest neighbors were still eligible to be substitutes, the one with a closer grade enrollment was chosen. If both nearest neighbors were equally distant from the sampled school in their grade enrollment (an uncommon occurrence), one of the two was randomly selected.
Less than five substitutes participated in grades 4 and 8, and about 20 for grade 12.