There is a lack of diagnostic credibility to direct focused management for children with chronic constipation (CC) and faecal incontinence (FI). The aim is to assess the impact of an innovative Children's Anorectal Physiology Service (CAPS) focusing on improving outcomes in children with CC/FI.Prospective data: demographics, bowel and quality of life (QoL)/risk of distress questionnaires. Diagnostics: awake high-resolution anorectal manometry (AHRAM), endoanal ultrasound and transit marker studies (TMS).Total patients: 112; 66 males (59%); median 9 years (17 months to 16 years). Patient groups included: 89 (79%) had functional CC/FI; 9 (8%), Hirschsprung's disease; 12 (11%), anorectal malformations and 2 (2%), trauma. St Marks Incontinence score (SMIS) abnormal in 91 (81%) and Cleveland Constipation Score (CCS) in 101 (90%) patients. Anorectal manometry: 94 (84%) awake and 18 (17%) under anaesthesia. Play specialist input 37 (33%) patients. AHRAM abnormal 65 (58%): sphincter dysfunction 36 (32%) and altered rectal sensation: hyposensitive 22% (20/91); 21% (19/91) hypersensitive. TMS normal in 64 (57%), 17 (15%) slow transit and 27 (24%) rectal evacuatory disorder. Risk of distress in 38% and poor QoL in 55% patients which correlated with abnormal SMIS (p = 0.02). Patient/parent satisfaction improved significantly (p < 0.05).Scientific investigations combined with multidisciplinary team improve patient satisfaction and reduces patient self-report illness severity. A complex problem requires a scientific solution.