Background Complete resection is critical for local control of primary bone sarcomas. Intraoperative consultation, including frozen section of bone marrow margins, frequently is used to aid in this goal. Questions/purposes We therefore sought to determine (1) how often intraoperative frozen section of a bone marrow margin correlates with inspection of the gross split specimen and, in cases of a discrepancy, what clinical decision is made; and (2) how well each of these assessments agrees with the final pathologic assessment of a marrow margin. Methods One hundred ninety-five bone marrow margins from 142 patients (74 males, 68 females; mean age, 12.8 years) with primary sarcomas who underwent resection and had frozen section(s) performed on a bone marrow margin were analyzed. Agreement between frozen section interpretation and inspection of the split gross specimen was analyzed in their application to determine adequacy of the bone marrow margin intraoperatively. Results In 179 margins, the frozen section agreed with the gross inspection decision (95.6% negative agreement, 38.5% positive agreement). Decisions regarding further surgical action in all 16 instances of disagreement were based on inspection of the split gross specimen, and the frozen section was disregarded. In 195 of 195 margins, intraoperative decisions were made based on gross specimen inspection.