Intraoperative consultation (IOC) with frozen section (FS) allows the surgeon to make therapy decisions during the operation. However, there is relatively little information on the use of IOC in skeletal lesions. We performed a retrospective study to examine the indications for IOC and compare the histological findings of FS and permanent paraffin section (PS) results to determine its clinical benefits. Ninety-seven consecutive cases evaluated between 2008 and 2011 were retrieved from IOC archives of our Pathology Department. In 79 % of the cases, there was no prior core needle biopsy (CNB), and IOC was performed to confirm the clinical or radiological diagnosis. In 5 (5 %) cases, no definitive result could be obtained with FS, and diagnosis was deferred. The reasons for a deferred diagnosis (DD) included poor section quality in two lipomatous lesions and the sample heterogeneity in the others. When adjusted for DD, FS and PS results showed 100 % concordance in terms of discriminating "benign vs. malignant" and defining diagnostic categories as "benign non-tumoral," "benign tumoral/tumor-like," "malignant primary tumor," "malignant metastatic tumor," or "hematopoietic malignancy." The presence of non-sclerotic osseous tissues does not have a significant adverse impact on the FS section quality and diagnosis made by FS. Thus, sections with diagnostic value can be obtained from bone lesions via FS. In this study, specific diagnoses were made in 88 % of the cases. We believe that IOC with FS can be safely performed in tertiary referral centers where there is a multidisciplinary team working in collaboration.