Small intestinal biopsies are part of the routine evaluation of children with chronic diarrhea and malabsorption, and are commonly performed via suction capsule. Because this technique entails x-ray exposure, longer procedure time, and technical failures, most small intestinal biopsies in adults are currently obtained via endoscopy. Endoscopy is believed to yield morphologically inferior specimens, and, therefore, its use for obtaining small intestinal biopsies in children has remained limited. The histological adequacy of biopsy specimens obtained in 30 children by endoscopy and in 30 children by suction capsule was compared. Biopsies were assessed for quality of orientation, size (length and depth), presence of Brunner's glands and crush artifact, and for the ability to confirm or exclude a mucosal abnormality. Small intestinal biopsies obtained via endoscopy were shown to yield tissue specimens that are histologically comparable to those obtained by suction capsule, and that are equally suitable for interpretation.