The diverse needs for digital auto-focusing systems have driven the development of a variety of focus measures. The purpose of the current study was to investigate whether any of these focus measures are biologically plausible; specifically whether they are applicable to retinal images from which defocus information is extracted in the operation of accommodation and emmetropization, two ocular auto-focusing mechanisms. Ten representative focus measures were chosen for analysis, 6 in the spatial domain and 4 transform-based. Their performance was examined for combinations of non-defocus aberrations and positive and negative defocus. For each combination, a wavefront was reconstructed, the corresponding point spread function (PSF) computed using Fast Fourier Transform (FFT), and then the blurred image obtained as the convolution of the PSF and a perfect image. For each blurred image, a focus measure curve was derived for each focus measure. Aberration data were either collected from 22 real eyes or randomly generated data based on Gaussian parameters describing data from a published large scale human study (n>100). For the latter data set, analyses made use of distributed computing on a small inhomogeneous computer cluster. In the presence of small amounts of nondefocus aberrations, all focus measures showed monotonic changes with positive or negative defocus, and their curves generally remained unimodal, although there were large differences in their variability, sensitivity to defocus and effective ranges. However, the performance of a number of these focus measures became unacceptable when nondefocus aberrations exceed a certain level.