The effects of poor anterior segment compensation on scanning laser polarimetry measurements of the retinal nerve fiber layer (RNFL) were systematically explored. A prototype scanning laser polarimeter with an adjustable compensator to neutralize anterior segment birefringence was used. By systematically varying the magnitude and axis of anterior segment compensation in a healthy and a glaucomatous eye, marked changes were observed in RNFL appearance: the healthy eye could appear to have glaucomatous damage, whereas the glaucomatous eye could appear to have a thicker and healthier RNFL. Even small amounts of uncompensated corneal birefringence, which may occur in routine clinical use, resulted in apparent changes in RNFL morphology. Knowledge of this effect is important for clinicians when using scanning laser polarimetry in clinical practice.