Although iron, vitamin B12, and folate deficiency have been well documented after gastric bypass operations performed for morbid obesity, there is surprisingly little information on either the natural course or the treatment of these deficiencies in Roux-en-Y gastric bypass (RYGB) patients. During a 10-year period, a complete blood count and serum levels of iron, total iron-binding capacity, vitamin B12, and folate were obtained in 348 patients preoperatively and postoperatively at 6-month intervals for the first 2 years, then annually thereafter. The principal objectives of this study were to determine how readily patients who developed metabolic deficiencies after Roux-en-Y gastric bypass responded to postoperative supplements of the deficient micronutrient and to learn whether the risk of developing these deficiencies decreases over time. Hemoglobin and hematocrit levels were significantly decreased at all postoperative intervals in comparison to preoperative values. Moreover, at each successive interval through 5 years, hemoglobin and hematocrit were decreased significantly compared to the preceding interval. Folate levels were significantly increased compared to preoperative levels at all time intervals. Iron and vitamin B12 levels were lower than preoperative measurements and remained relatively stable postoperatively. Half of the low hemoglobin levels were not associated with iron deficiency. Taking multivitamin supplements resulted in a lower incidence of folate deficiency but did not prevent iron or vitamin B12 deficiency. Oral supplementation of iron and vitamin B12 corrected deficiencies in 43% and 81% of cases, respectively. Folate deficiency was almost always corrected with multivitamins alone. No patient had symptoms that could be attributed to either vitamin B12 or folate deficiency Conversely, many patients had symptoms of iron deficiency and anemia. Lack of symptoms of vitamin B12 and folate deficiency suggests that these deficiencies are not clinically important after RYGB. Conversely, iron deficiency and anemia are potentially serious problems after RYGB, particularly in younger women. Hence we recommend prophylactic oral iron supplements to premenopausal women who undergo RYGB.