Although the between-day differences in tear protein levels were not statistically significant, the variations in some proteins would be large in magnitude. The variability of tear protein levels obtained by the eye-flush method was larger than that by the yawn method. Therefore, caution should be taken if the eye-flush method is used for sampling tears for quantitative analysis of tear proteins, although it is easier to collect tear samples using this method. The results will be useful to exclude normal variation in tear protein levels when comparing pre- and post-therapeutic tear protein levels in eyes treated for tear-related abnormalities.