Anorectal malformations (ARM) are a spectrum of anomalies of the rectum and anal canal affecting 1 in 2500 to 5000 live births. Functional problems are common and related to the type of ARM and associated malformations. We aimed to evaluate the results of Three-dimensional High Resolution Anorectal Manometry (3D-HRAM) in long-term follow-up after surgical correction of ARM with special reference to fecal incontinence. Twenty-one patients with anorectal malformations and primary repair at our center consented to participate in the study. Pressures of the anal sphincter muscles and defects were addressed by 3D-HRAM. Fecal incontinence and disease-specific quality of life were evaluated by the Fecal Incontinence Quality of Life score and Wexner incontinence score respectively. The study was approved by the Committee in Health Research Ethics and the Danish Data Protection Agency. Median age was 22(12–31) years and 13(67%) participants were females. Sphincter defect was present in 48% (N = 10) of participants. Participants with sphincter defects had significant higher Wexner score and size of sphincter defects and mean anal squeeze pressure were correlated to Wexner score. Participants with or without sphincter defects did not differ on manometry parameters including resting anal and squeeze pressure or disease-specific quality of life. In a study of the long-term outcome after repair of anorectal malformations we found a higher Wexner incontinence score in the presence of an anal sphincter defect and the size of the defect and mean anal squeeze pressure were correlated to the Wexner incontinence score.