The pathogenesis of slow transit constipation is still elusive. However, a genetic basis may be present. We investigated possible chromosomal abnormalities in enteric neurons and glial cells in patients with slow transit constipation. Colonic specimens from 22 patients with slow transit constipation undergoing surgery for intractable symptoms were obtained, and investigated by fluorescence in situ hybridization (FISH) for chromosomal abnormalities (chromosomes 1, 8, 17 and XY). These specimens were compared with of those obtained in 12 control subjects. Data analysis showed that 45.5% of patients displayed significant (>10%) aneusomy of chromosome 1 in enteric neurons. Aneusomy <10% for the same chromosome, but less than the cutoff suggested (10%), was found in enteric glial cells in 45.4% of the same patients. One patient had <10% aneusomy in enteric neurons for chromosome 8. No other abnormalities were found for the remaining probes, and no abnormalities were found in controls. We concluded that in a subgroup of patients with slow transit constipation a genetic basis may be present.