BACKGROUND: Autorefractors are increasingly used in myopia research because they are convenient tools to investigate aspects of the accommodation response. The degree to which the autorefractor measures are affected by ocular aberrations has been highlighted by studies that have shown changes in aberration levels through different parts of the pupil and with accommodation. We have compared accommodative accuracy as measured with a Shin-Nippon SRW 5000 autorefractor with wavefront error as measured with a Hartmann-Shack wavefront sensor to investigate how factors such as accommodation demand, ocular aberrations, and pupil size can influence autorefractor measures. METHODS: Accommodation stimulus-response curves were determined (using negative lenses) for 30 young healthy subjects (20 myopic [-0.75 to -6.00 D] and 10 emmetropic). Accommodation levels ranged from 0 to 4 D in 1 D steps. Wavefront aberrations were also determined for the same accommodation levels using a Hartmann-Shack wavefront sensor for both the subjects' natural pupil sizes and for a 2.9-mm pupil. RESULTS: For all subjects, there was a consistent increase in negative spherical aberration with increases in accommodative stimulus. However, there was no consistent change in paraxial spherocylindrical refractive correction with accommodation stimulus. For the emmetropic subjects, accommodation error as measured with the autorefractor was statistically similar to the total spherocylindrical correction for the eye as estimated by the Hartmann-Shack wavefront sensor, but only for a 2.9-mm pupil (the pupil size utilized by the autorefractor). For the myopic subjects, accommodation error as measured with the autorefractor was statistically similar to the higher-order aberrations, but only when measured for a natural pupil size. CONCLUSIONS: The relationship between the accommodation accuracy as measured with the autorefractor and the total wavefront aberration as measured with a Hartmann-Shack wavefront sensor is largely influenced by the higher-order (fourth and above) aberration levels. For the emmetropic subjects, the errors measured by the two methods agree when adjusted to measure at similar pupil sizes. For the myopic subjects with similar pupil sizes, however, the Hartmann-Shack wavefront sensor underestimates the accommodation error at higher accommodation levels (2 to 4 D) compared with the autorefractor.