The pupil diameter under low ambient illumination is diagnostically valuable for refractive surgery. The aim of study was to compare the NeurOptics® Pupillometer, Sirius®, and Ocular Wavefront Analyser® in determining scotopic pupil diameter. A total of 96 eyes of 48 subjects were included. The scotopic pupil size was measured with 3 instruments and the measurements repeated following instillations of 1% cyclopentolate. Agreement between the instruments was assessed. The mean measurement obtained by Sirius was significantly larger than Ocular Wavefront Analyser and NeurOptics. The Ocular Wavefront Analyser measured significantly smaller than the others. The mean cycloplegic pupillary diameters (7.73±0.70 mm with NeurOptics, 7.42±0.45 mm with Ocular Wavefront Analyser, and 8.06±0.76 mm with Sirius) were significantly different obtained by 3 instruments (p<0.001, for each; one-way analysis of variance and paired t tests). The differences between measured pupil diameters with or without cycloplegia obtained by the NeurOptics, Sirius, and Ocular Wavefront Analyser were significant and have unacceptable levels of disagreement. These results may not be related to illumination and accommodation only, but also to measurement algorithms and technical differences of the devices.