Clinicians measure the near point of convergence (NPC) and the amplitude of accommodation (AA) from the spectacle plane, the bridge of the nose or the lateral canthus when assessing visual function. These values are compared to standard clinical criteria to diagnose vergence and accommodation deficits, despite varying reference points. This prospective study explored measuring relative to the spectacle plane and from the lateral canthus for NPC and monocular AA, and the resulting clinical implications of diagnosing visual deficits. Participants were seen by a single clinician for an eye examination. NPC was measured from the forehead and the lateral canthus of the right eye. Monocular AA was measured from the brow and the lateral canthus. Differences between measurements were analysed using non-parametric statistical tests including Wilcoxon Signed Rank, as well as linear regression and a linear mixed effects model to adjust for inter-eye correlation and repeated measures. Chi-square tests were used to assess differences in rates of abnormal findings. Data were collected from 70 participants (53% female, median age 13 [11-15] years). On average, measuring NPC from the lateral canthus yielded a value 1.8 cm higher than measuring from the forehead. Measuring AA from the lateral canthus resulted in an average difference of 1.5 cm compared to measuring from the brow. A total of 39% and 76% of subjects failed NPC compared to clinical norms when measured from the forehead or the lateral canthus, respectively, while 7% and 40% failed AA when measured from the brow or the lateral canthus, respectively. With the variable anatomy of the eye, it is imperative to account for the measurement point when assessing visual function. Measuring from the lateral canthus greatly increased the failure rates for NPC and AA compared with measuring from the forehead and brow, respectively.