Spontaneous small intestinal perforations are common in India. Surgeons operating on patients with an obscure peritonitis should be aware of the diverse aetiologies of small intestinal perforations in order to be able to provide the appropriate management. We reviewed the pathology records of 165 patients operated on for nontraumatic perforations of the small intestines in our hospital between 2005 and 2007. Perforation edge biopsy was diagnostic in 53 cases, with typhoid being the most common aetiology, followed by TB. The majority of cases, however, revealed only a non-specific inflammatory granulation tissue. However, the sensitivity of biopsy diagnosis could be increased by taking additional biopsy material from the mesenteric lymph nodes, tubercles or omental nodules. We conclude that perforation edge biopsy is useful in a third of cases, but the diagnostic rate could be improved by taking additional biopsy material.