Substitute schools were preselected for the private school samples by sorting the school frame file according to the actual order used in the sampling process (the implicit stratification). 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; the nearest neighbors had grade enrollment values very close to that of the sampled school.
Schools were disqualified as potential substitutes if they were already selected in the private school sample or assigned as a substitute for another private 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. See the NAEP 2006 Sample Design for more information about PIRLS.
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.
About 20 substitute schools participated in each grade.