Pyogenic liver abscesses are rare in children, and show geographical differences in their epidemiology. Mortality rates remain high at 15 %. Liver abscesses caused by anaerobic organisms are rare in a paediatric setting, even more so when complicated by portal vein thrombosis (PVT). A 6-year-old girl, previously fit and well, was admitted with fever, lethargy and weight loss of 2 weeks duration. The patient was febrile on examination and a review of the systems revealed no positive findings. An abdominal ultrasound scan showed multiple interconnecting cystic lesions consistent with liver abscesses, which was confirmed by a computed tomography scan. Aspirate of the abscess was cultured, resulting in the isolation of a non-haemolytic anaerobic organism, which was difficult to identify using conventional phenotypic identification tests. 16S rRNA typing identified the organism as Clostridium clostridioforme. The liver abscess in our patient displayed a particularly aggressive clinical course with extension of the abscess to involve the upper pole of the right kidney and the appendix, which was further complicated by PVT. The role of anaerobic organisms in liver abscesses has been underreported in the past. This case, therefore, highlights the importance of incubating biological samples in anaerobic conditions in order to adequately isolate and identify anaerobic bacteria, particularly those associated with abscesses.