Chronic idiopathic constipation and abdominal pain are the most common gastrointestinal symptoms but their cause is rarely determined; therefore, they usually are called functional. To determine if congenital factors play a role in these disorders, we examined dermatoglyphic (fingerprint) patterns, a congenital marker, in 155 consecutive patients with gastrointestinal complaints. Sixty-four percent of patients with constipation and abdominal pain before age 10 yr had one or more digital arches, compared with 10% of patients without constipation and abdominal pain (p less than 0.001). Seventy percent of constipated patients with arches had the onset of symptoms before age 10 yr compared with 23% of constipated patients without arches (p less than 0.001) and 14% of patients with symptoms other than constipation (p less than 0.001). Compared with an age- and sex-matched sample of patients without arches, patients with arches had a higher prevalence of constipation and abdominal pain before age 10 (p = 0.003), were more likely (p less than 0.001) to have chronic intestinal pseudoobstruction (an organic disorder), and were less likely (p = 0.013) to have irritable bowel syndrome (a functional disorder). Identification of a congenital marker, digital arches, associated with early onset constipation and abdominal pain may help to differentiate a congenital organic syndrome from functional disorders such as the irritable bowel syndrome.