Physiotherapy and radiography of the joints are standard diagnostic strategies for assessment of haemophilic arthropathy. The use of ultrasonography as an adjunct tool for early diagnosis of haemophilic arthropathy may optimize factor replacement therapy. The objective of this study was to compare costs and effectiveness of physiotherapy, radiography and ultrasonography (intervention strategy, IS) with physiotherapy and radiography alone (standard care strategy, SCS) for diagnosing soft tissue and osteocartilaginous changes in haemophilic joints. We retrospectively compared costs and effectiveness of IS vs. SCS in knees, ankles and elbows of 31 children (age range, 4-17 years) with haemophilia A (n = 30) or B (n = 1) (IS, n = 11; SS, N = 20). Direct health care costs were measured from the provincial health care perspective. Effectiveness was measured by false-negative (FN) rates in each study arm by comparing presence or absence of abnormalities of physiotherapy and imaging exams to the reference standard measure (MRI). In scenario 1, all diagnostic tests matched with MRI. In scenario 2, at least one diagnostic test matched with MRI. The IS was more costly [incremental cost/100 patients, Canadian (CND) $4987] and more effective (incremental effectiveness, FNs/100 patients for scenario 1, -4.09, and for scenario 2, -41) for both scenarios. The incremental cost-effectiveness ratios for scenario 1 and for scenario 2 were CND$1166 and CDN$116 per FN result averted per 100 patients, respectively. In conclusion, in the short-term, the incorporation of ultrasonography in a test set for diagnosis of haemophilic arthropathy substantially improved the diagnostic performance of this test set, however at an increased cost.