Background <p>There is a wide spectrum of anorectal malformations (ARMs). The majority of ARM types can be diagnosed thorough perineal examination and radiological investigations such as MRI and distal loopogram. The most important aim of ARM repair is keeping the rectum in the muscle complex to protect continence, but still there are important factors that influence continence such as spine anomalies and associated urological anomalies.</p> Case presentation <p>In our report we describe two patients with ARM and abnormal anal sphincteric locations. The first case was a two-year-old female patient who presented with a massive perineal mass and peculiar female external genitalia that covers the entire perineum. Examination under general anaesthesia (EUA) revealed an extensive perineal lipoma that extends from the posterior point of the coccyx to the middle anterior separated pubic bone overlying a cavity separating it from a normal vaginal introitus containing normal urethral meatus, bicuspid Hymen and anorectal malformation with a vestibular fistula. MRI pelvis showed a large perineal lipoma. Surgical removal of the perineal mass, restoration of the perineal body and external genitalia, and anorectoplasty were performed. The second case was a 13-year-old male who is known to have bladder exstrophy but presented with mucosal bridges producing mucous and abnormally located anus. Excision of the mucosal bridge and confirming the accurate location of the anus within the muscle complex was performed.</p> Conclusions <p>It is important to look for and put into consideration other anomalies which can be associated with ARMs and influence the continence, in addition, to accurately locating the sphincter muscle complex using muscle stimulation to ensure placement of the anus within the complex to provide the best bowel function outcome for these cases.</p>