The number of cystic fibrosis (CF) patients undergoing lung transplant has risen over the past decade, because of a clear-cut survival benefit. However, patients with Burkholderia cepacia complex are often excluded from transplantation because of increased mortality. To determine the influence of B. cepacia complex genomovar type on transplant outcome, we undertook a retrospective study in 121 CF patients transplanted at UNC. Twenty-one and three patients, respectively, were infected pre- or postoperatively with B. cepacia complex. All posttransplant acquisitions were successfully treated. However, excess mortality occurred over the first 6 postoperative months in those infected preoperatively with B. cepacia complex compared with those not infected (33% versus 12%, p = 0.01). The 1-, 3-, and 5-yr survival were significantly lower in the B. cepacia complex cohort. Of the patients infected preoperatively, genomovar III patients were at the highest risk of B. cepacia complex-related mortality (5 of 12 versus 0 of 8, one isolate not typed; p = 0.035). Each of the B. cepacia complex-related deaths was caused by a unique genotype as determined by pulsed-field gel electrophoresis. All isolates were negative for the cable pilin gene. These results warrant a multicenter analysis of B. cepacia complex-infected patients with genomovar-typing to confirm that genomovar III patients are at highest risk for post-transplant complications.