AIM: To explore whether low myopia would affect cerebral visual functions by comparing perceptual eye position (PEP), fixation stability and stereoacuity tests between low myopic and normal adolescents. METHODS: Totally 120 adolescents matched in age and gender participated in our study. Subjects were divided into three groups according to their refractive states. The cerebral visual functions tested in our study included perceptual eye position (PEP), fixation stability and stereoacuity. Stereoacuity tests involved in our study could be categorized into two parts. The first part was classical stereo tests including Titmus and synoptophore stereo test. The second part was 3D random-dot test for zero-order stereoacuity (hereinafter as zero-order test) at different viewing distances (0.8 m and 1.5 m). RESULTS: The deviation of horizontal PEP was significantly larger in non-anisometropia when compared to control group. Both horizontal and vertical PEP bias pixels were significantly larger in anisometropia group. Both non-anisometropia group and anisometropia group had more trouble in holding their fixation stable. Moreover, anisometropia group had more abnormal results than other two groups. And in zero-order test at 1.5 m, both non-anisometropia and anisometropia had more abnormal results in stereoacuity than control group. The correlation between fixation stability and near stereoacuity (Titmus and zero-order stereoacuity at 0.8 m) was weak and positive. CONCLUSION: Low myopic adolescents still have certain defects in cerebral visual functions. Examinations used in our study are useful in assessing cerebral visual functions. They could provide better follow-up evaluation and solid ground for further specific treatments in treating defects of cerebral visual functions. So far, local retinal environment has been the focus of the development in myopia. Our results suggested that researchers might pay more attention on visual cortex in studying the mechanisms of myopia in the near future.