The objective of this study was to evaluate patient perception of endoanal MRI compared with defecography and anorectal functional testing in the workup of patients with faecal incontinence. Consenting consecutive patients underwent a standard testing protocol consisting of endoanal MRI, defecography and anorectal function combination. Patient experience was evaluated with a self-administered questionnaire, addressing anxiety, embarrassment, pain and discomfort, each measured on a 1 (none) to 5 (extreme) point-scale. Patients were also asked to rank the three tests from least to most inconvenient. Statistical analysis was performed with parametric tests. Data from 211 patients (23 men; mean age 59 years (SD+/-12)) were available. MRI had the lowest average score for embarrassment and discomfort (1.6) and defecography the highest (1.9 and 2.0, respectively) (p<0.0001, tested with general linear model for related samples). The average pain score was lowest for MRI (1.4) and highest for the anorectal function combination (1.7) (p<0.0001). Level of anxiety was highest for MRI (1.6 versus 1.4; p = 0.03). MRI was scored as least inconvenient by 69% of patients. Endoanal MRI was scored as least inconvenient. However, the differences in patient burden between the three diagnostic tests were small and absolute values were low for all tests. Patient perception will not be a key feature in determining an optimal diagnostic strategy in faecal incontinence.