Chondromyxoid fibromas can share characteristics with chondroblastomas with regards to histologic and radiographic findings. However they more commonly originate from the metaphysis, lack calcification and have a different histologic organization pattern. Other differential diagnoses for chondroblastoma consist of giant cell tumors, bone cysts, eosinophilic granulomas, clear cell chondrosarcomas, and enchondromas (this list is not exhaustive).

Chondroid differentiation is a common feature of chondroblastoma. A typical histological appearance consists of a combination of oval mononuclear and multi-nucleated osteoclast-type giant cells. However this is not a prerequisite for diagnosis, as cells with epithelioid characteristics have been observed in lesions of the skull and facial bones. A "chicken-wire" appearance is characteristic of chondroblastoma cells and is the result of dystrophic calcification that may surround individual cells. Although, calcification may not be present and is not a prerequisite for diagnosis. Mitotic figures can be observed in chondroblastoma tissue but are not considered atypical in nature, and therefore, should not be viewed as a sign of a more serious pathology. There is no correlation between mitotic activity and location of the lesion. Furthermore, the presence of atypical cells is rare and is not associated with malignant chondroblastoma. There are no discernible histological differences observed when comparing the aggressive form of chondroblastoma that can cause recurrence or metastases with its less aggressive, benign, counterpart.

On X-ray, giant-cell tumors (GCTs) are lytic/lucent lesions that have an epiphyseal location and grow to the articular surface of the involved bone. Radiologically the tumors may show characteristic 'soap bubble' appearance. They are distinguishable from other bony tumors in that GCTs usually have a nonsclerotic and sharply defined border. About 5% of giant-cell tumors metastasize, usually to a lung, which may be benign metastasis, when the diagnosis of giant-cell tumor is suspected, a chest X-ray or computed tomography may be needed. MRI can be used to assess intramedullary and soft tissue extension.

Recurrence rate of solid form of tumour is lower than classic form.

The diagnosis of giant-cell tumors is based on biopsy findings. The key histomorphologic feature is, as the name of the entity suggests, (multinucleated) giant cells with up to a hundred nuclei that have prominent nucleoli. Surrounding mononuclear and small multinucleated cells have nuclei similar to those in the giant cells; this distinguishes the lesion from other osteogenic lesions which commonly have (benign) osteoclast-type giant cells. Soap-bubble appearance is a characteristic feature.

Following conditions are excluded before diagnosis can be confirmed:

- Unicameral bone cyst

- Giant cell tumor

- Telangiectatic osteosarcoma

- Secondary aneurysmal bone cyst

Many types of blastoma have been linked to a mutation in tumor suppressor genes. For example, pleuropulmonary blastomas have been linked to a mutation of the coding for p53. However, the mutation which allows proliferation of incompletely differentiated cells can vary from patient to patient and a mutation can alter the prognosis. In the case of retinoblastoma, patients carry a visibly abnormal karyotype, with a loss of function mutation on a specific band of chromosome 13. This recessive deletion on the rb gene is also associated with other cancer types and must be present on both alleles, for a normal cell to progress towards malignancy.

A blastoma is a type of cancer, more common in children, that is caused by malignancies in precursor cells, often called blasts. Examples are nephroblastoma, medulloblastoma and retinoblastoma. The suffix "-blastoma" is used to imply a tumor of primitive, incompletely differentiated (or precursor) cells, e.g., chondroblastoma is composed of cells resembling the precursor of chondrocytes.