Hepatic dysfunction following hematopoietic stem cell transplantation (SCT) is common, but making the correct diagnosis can be challenging.When the etiology cannot be determined by laboratory data, physical examination, and imaging studies, liver biopsies serve as an important diagnostic tool. In the immediate post SCT setting, cytopenias, coagulopathy, along with tissue injury and friability significantly increase the risk of bleeding and poor wound healing following percutaneous or "open" biopsies. At our institution, laparoscopic-guided liver biopsy (LGLB) is the preferred technique for pediatric SCT patients. Laparoscopy offers multiple benefits such as minimal invasiveness, faster recovery, better surgical hemostasis, superior visualization of the liver and peritoneal cavity, and the ability to assess for pathology confined to lobar segments. Little data exist on the feasibility of this technique in pediatric SCT patients. We reviewed the course of 11 consecutive patients (6 male, 5 female, age range 9–23 years) who received allogeneic SCT and subsequently underwent LGLB between 1998 and 2004 for hepatic dysfunction of unknown etiology. The time from SCT to LGLB ranged from 23 to 405 days (median 97 days) and 8 (73%) patients were biopsied within 106 days of SCT. Seven (64%) patients had platelet counts less than 100,000/mm3. Biopsies were performed using a single port technique. After visual inspection of the peritoneal cavity, a 16 or 18 gauge spring loaded biopsy gun (Monopty Biopsy instrument, CR Bard Inc., Covington, GA) was passed through a small stab wound in the right upper quadrant, and then directed to the right lobe of the liver. A total of 4 to 5 core biopsies were routinely obtained and specimens were subsequently sent fresh to the pathology department for processing and review. No intra- or post-operative complications were observed. The initial clinical diagnosis was confirmed in 5 patients. In one patient, veno-occlusive disease (VOD) was substantiated by evidence of bridging fibrosis, whereas in the other 4 patients, histopathologic findings were consistent with the diagnosis of GVHD. Of particular interest, biopsy results demonstrated that the initial working diagnosis was incorrect in the remaining 6 (55%) patients. In 4 of these 6 patients, the clinical diagnosis was hepatic GVHD, but histologic examination demonstrated that the actual causes of liver dysfunction were iron overload, VOD, cholestatic liver disease of unclear etiology, and hepatocyte injury secondary to drug toxicity or infection. In the two other patients, the clinical diagnosis was unresolved in one and the patient was found to have GVHD, whereas the other individual was initially diagnosed with infectious hepatitis, but was ultimately found to have hepatitis secondary to massive iron overload. Our results suggest that LGLB in pediatric patients experiencing liver dysfunction after SCT can be informative and safe. LGLB helped delineate the true cause of hepatic dysfunction and changed our approach to therapy in more than 50% of the patients reviewed. Results from LGLB thus maximized therapeutic efficiency and minimized the exposure of our patients to unnecessary toxicity including the profound risk of infection that accompanies immunosuppressive therapy.