In this article, indications and pitfalls in frozen section diagnosis in selected organs and systems are discussed. The main indications for frozen section examination of head and neck and genitourinary system lesions are to evaluate the resection margin and the metastatic involvement of lymph nodes. Recently, intraoperative consultation has been introduced for identification of patients who might benefit from testis-sparing surgery. Preoperative fine-needle aspiration has greatly diminished the need for frozen section evaluation of thyroid lesions. The only reasonable indication for intraoperative examination of the thyroid is a lesion suspected of malignancy for which preoperative cytology is not aviable for various reasons. In contrast, frozen section is still routinely requested at many institutions to confirm the presence of parathyroid lesions, although precise differentiation between parathyroid hyperplasia, adenoma, and carcinoma is not possible in most cases by histological assesment alone. Tumors of bone and soft tissue are relatively rare, and most pathologists are unfamiliar with intraoperative consultation of these lesions. However, in many cases, limb-sparing management of bone and soft tissue sarcomas is dependent on intraoperative histological diagnosis. Accurate diagnosis is possible in most instances by correlating the histology with clinical and radiological data. In selected cases, histochemistry and/or intraoperative immunohistochemistry may be helpful in diagnosis of bone lesions. Keywords: frozen section - head and neck - thyroid gland - parathyroid gland - soft tissue - urogenital tract.