Background Faecal incontinence is common and of multifactorial aetiologies, yet current diagnostic tools are unable to objectively assess nerve and sphincter function. We developed and evaluated anorectal high-density electromyography (HD-EMG) of motor-evoked potentials via trans-sacral magnetic stimulation (TSMS). Methods Anorectal probes with an 8x8 array of 1 cm spaced electrodes were developed for recording HD-EMG of the external anal sphincter. HD-EMG probes were used to map motor-evoked potential (MEP) amplitudes and latencies evoked via TSMS delivered through the Magstim Rapid² (MagStim Company, Dyfed, UK). Patients undergoing pelvic floor investigations were recruited for this IDEAL Stage 2a pilot study. Results Eight participants (5 female, median age 49) were recruited. Methodological viability, safety, and diagnostic workflow were established. The test was well tolerated with median discomfort scores ≤2.5/10, median pain scores ≤1/10 and no adverse events. Higher faecal incontinence severity index scores correlated with longer MEP latencies (r = 0.58, p <0.001) and lower amplitudes (r = -0.32, p=0.046), as did St Mark’s incontinence scores with both MEP latencies (r = 0.49, p = 0.001) and MEP amplitudes (r = -0.47, p = 0.002). Conclusion This high-density EMG probe in conjunction with trans-sacral magnetic stimulation presents a novel diagnostic tool for anorectal function assessment. Spatiotemporal assessment of magnetically stimulated MEPs correlated well with symptoms and offer a feasible, safe, and patient tolerable method of evaluating pudendal nerve and external anal sphincter function. Further clinical development and evaluation of these techniques is justified.