Purpose: We sought to compare intraocular pressure (IOP) measurements by Perkins tonometer and Tono-Pen in young children with primary congenital glaucoma (PCG). Methods: This was a retrospective comparative case series. We reviewed the clinical records of all children with primary congenital glaucoma who underwent examinations under general anesthesia at Soroka University Medical Center between January 1999 and July 2002. Our main outcome measures were IOP with Perkins hand-held tonometer and Tono-Pen tonometer. Results: A total of 28 eyes of 16 children were examined under general anesthesia. The mean IOP was 18 ± 6 mm Hg with the Perkins tonometer and 22 ± 8 mm Hg with the Tono-Pen. In 18 eyes, IOP was less than 21 mm Hg with the Perkins tonometer; these eyes had already undergone surgical procedures. The other 10 eyes with IOP greater than 21 mm Hg with the Perkins tonometer underwent surgery at the end of the examination under anesthesia. In eyes with IOP greater than 16 mm Hg (Group A, n = 18), a significant difference (P < 0.001) was found between the Perkins and Tono-Pen measurements, even although the values were strongly correlated (r = 0.60). In contrast, in eyes with IOP less than 16 mm Hg (Group B, n = 10) no statistically significant difference (P = 0.28) and good correlation (r = 0.78) were obtained. A difference of 5.8 ± 3.8 mm Hg and 0.6 ± 1.7 mm Hg between Perkins and Tono-Pen readings, respectively, was found in Groups A and B. Conclusions: Tono-Pen readings disagree with Perkins tonometer measurements for measuring IOP in children with PCG who present with IOP greater than 16 mm Hg and tends to overestimate IOP. A further study with a similar population is necessary to confirm these results.