We compared the cost-effectiveness of fluoroscopically directed percutaneous needle biopsy (PNB) of musculoskeletal lesions, CT-guided PNB, and open biopsy. We independently assessed the following characteristics: suspected lesion type (metastatic deposit, infection, or primary neoplasm, as determined by clinical findings and radiologic appearance before biopsy); lesion location (axial or appendicular); and appearance on plain films (radiolucent or lytic, sclerotic, vertebral compression fracture, and soft-tissue lesions). In suspected primary tumors, cost-effectiveness of PNB was similar to that of open biopsy: fluoroscopically directed PNB was slightly more cost-effective than open biopsy whereas CT-directed PNB was slightly less cost-effective. Either type of PNB was cost-effective for suspected metastatic deposits and infections, axial and appendicular lesions, radiolucent or lytic lesions, and soft-tissue lesions. We conclude that PNB is cost-effective for most musculoskeletal lesions.