Twenty-eight patients undergoing jejunoileal bypass for morbid obesity were studied prospectively for alterations in mineral metabolism and the development of metabolic bone disease. Eleven additional patients were examined for long-term complications. Serum 25-hydroxyvitamin D and fractional calcium absorption were depressed during the first 2 yr after bypass but normalized after this period. Serum parathormone remained normal. Mild osteomalacia was identified in 12% of subjects by histomorphometric analysis of undecalcified biopsy specimens. Osteomalacia was asymptomatic and could not be reliably diagnosed by noninvasive tests. Repeat biopsies demonstrated histologic improvement in 2 individuals followed serially. Improvement was not clearly related to vitamin D therapy. Abnormalities in mineral appositional rates and mineral maturation were identified in several additional patients. Studies in the long-term group did not indicate inexorable progression of metabolic bone disease. Although intestinal bypass produced several abnormalities in mineral metabolism during the first 2 yr after surgery, a trend toward normalization was evident after the period, possibly related to adaptive responses in the intestine.