Background Amblyopia is a common ophthalmological condition and the wavefront aberrometer is a relatively new diagnostic tool used globally to measure optical characteristics of human eyes as well as to study refractive errors in amblyopic eyes. We studied the wavefront aberration of the amblyopic children's eyes and analyzed the mechanism of the wavefront aberration in the formation of the amblyopia, try to investigate the new evidence of the treatment of the amblyopia, especially in the refractory amblyopia. Methods The WaveScan Wavefront System (VISX, USA) aberrometer was used to investigate four groups of children under dark accommodation and cilliary muscle paralysis. There were 45 cases in the metropic group, 87 in the amblyopic group, 92 in the corrected-amblyopic group and 38 in the refractory amblyopic group. One-way analysis of variance (ANOVA), t-test and multivariate linear regression were used to analyze all the data. Results Third order to 6th order aberrations showed a decreasing trend whereas in the higher order aberrations the main ones were 3rd order coma (Z(3)(-1)-Z(3)(1)), trefoil (Z(3)(-3)-Z(3)(3)) and 4th order aberration (Z(4)(0)); and 3rd order coma represented the highest percentage of all three main aberrations. Within 3rd order coma, vertical coma (Z(3)(-1)) accounted for a greater percentage than horizontal coma (Z(3)(1)). Significant differences of vertical coma were found among all clinical groups of children: vertical coma in the amblyopic group (0.17+/-0.15) was significantly higher than in the metropic group (0.11+/-0.13, P <0.05). In addition, the vertical coma in the refractory amblyopic group (0.19+/-0.15) was higher compared with the metropic group (P <0.05), the 5th order aberration (0.11+/-0.08) was also significantly higher than in the metropic group (0.07+/-0.04, P <0.05). No significant difference was found in vertical coma and 5th order aberration between the corrected-amblyopic group (0.13+/-0.11) and metropic group (0.07+/-0.04) (P >0.05). Conclusions Although lower order aberrations such as defocus (myopia and hyperopia) and astigmatism are major factors determining the quality of the retinal image, higher order aberrations also need to be considered in amblyopic eyes as their effects are significant. Chin Med J 2010;123(11):1431-1435