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Abstract Background Periprosthetic joint infection (PJI) is a severe complication following knee arthroplasty. Therapeutic strategies comprise a combination of surgical and antibiotic treatment modalities and aim to eradicate the infection. Sometimes control of the disease can only be attained by above-knee amputation (AKA). While a vast amount of literature exists illuminating predisposing factors for PJI, risk factors favoring the endpoint AKA in this context are sparsely known. Methods The purpose of this investigation was to delineate whether patients with PJI of the knee present specific risk factors for AKA. In a retrospective case-control study 11 cases of PJI treated with AKA were compared to 57 cases treated with limb salvage (LS). The minimum follow-up was 2 years. Comorbidities, signs and symptoms of the current infection, factors related to previous surgeries and the implant, microbiology, as well as therapy related factors were recorded. Comparative analysis was performed using student’s t-test, chi-square test or Fisher’s exact test. Binary differences were calculated using odds ratio (OR). Reoperation frequency was compared using Mann-Whitney U test. In-depth descriptive analysis of 11 amputees was carried out. Results A total of 68 cases aged 71 ± 11.2 years were examined, 11 of which underwent AKA and 57 had LS. Severe comorbidities (p = 0.009), alcohol abuse (p = 0.015), and preoperative anemia (p = 0.022) were more frequently associated with AKA. Preoperative anemia was found in all 11 amputees (100%) and in 33 of 57 LS patients (58%) with an average preoperative hemoglobin of 99.9 ± 15.1 g/dl compared to 118.2 ± 19.9 g/dl (p = 0.011). No other parameters differed significantly. AKA patients underwent a median of eight (range 2–24) reoperations, LS patients a median of five (range 2–15). Conclusion Factors potentially influencing the outcome of knee PJI are diverse. The indication of AKA in this context remains a rarity and a case-by-case decision. Patient-intrinsic systemic factors such as alcohol abuse, severe comorbidities and preoperative anemia may elevate the individual risk for AKA in the setting of PJI. We recommend that anemia, being a condition well amenable to therapeutic measures, should be given special consideration in management of PJI patients. Trial registration This study was registered with Kantonale Ethikkommission Zürich, (BASEC-No. 2016–01048).