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A correlation exists between external anal sphincter (EAS) damage during birth and the subsequent development of fecal incontinence. This study evaluated the effect of delivery-related trauma on EAS innervation by means of intra-anal EMG performed with a rectal probe with 16 silver electrodes equally spaced along the circumference, before and after delivery. Pre-partum EMG measurements were performed on 511 women, by nine clinical partners from five European countries at the 28th to 34th gestational weeks and the 6th to 8th post-delivery weeks; 331 women returned, after delivery, for the second test. The innervation zones (IZ) of EAS single motor units were identified by means of an EMG decomposition algorithm. The subjects were divided into four groups according to the delivery mode (Caesarean, vaginal with no evident damage, spontaneous lacerations and episiotomies). The number of IZs before and after delivery was compared. In the 82 women who underwent right mediolateral episiotomy, a statistically significant reduction of IZs was observed, after delivery, in the right ventral quadrant of the EAS (side of the episiotomy). Women who had Caesarean section, spontaneous lacerations or lack of evident damage did not present any significant change in the innervation pattern. Right episiotomy reduces the number of IZs on the right-ventral side of the EAS. The fast and reliable test proposed indicates the sphincter innervation pattern before delivery and helps obstetricians to evaluate the risks and to choose the preferred side of the episiotomy, if deemed necessary at the time of delivery.