Two forms of tartrate-resistant acid phosphatase (TRACP) circulate in human blood, TRACP 5a derived from inflammatory macrophages and TRACP 5b derived from osteoclasts. Serum TRACP 5b is a clinically useful marker of osteoclast number and bone resorption. We have studied TRACP 5b specificity of two commercially available immunoassays that are stated to be TRACP 5b specific, the BoneTRAP assay and the MetraTRAP5b assay, and investigated their clinical performance for monitoring the efficacy of alendronate treatment. Both assays bound TRACP 5b equally and had similar cross-reactivity to TRACP 5a. The mean decrease in the alendronate group was higher with the MetraTRAP5b assay, but the clinical performance of the two assays for monitoring alendronate treatment was equal due to higher variability of the MetraTRAP5b assay. We conclude that the BoneTRAP assay and the MetraTRAP5b assay have similar specificity for TRACP 5b, and similar clinical performance for monitoring alendronate treatment.