Deletions on the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q) are molecular hallmark lesions of oligodendroglial tumors. Ever since oligodendroglial tumors with 1p and 19q deletions were shown to respond to chemotherapy, neuropathologists have been facing increasing requests for such molecular analysis. Therefore, there is increasing demand for reliable and simple assays. This brief report compiles information on different technical approaches, including manual and automated loss of heterozygosity analysis, fluorescence in situ hybridization techniques, and quantitative polymerase chain reaction. Herein we present a detailed protocol describing loss of heterozygosity analysis with microsatellite markers currently in use for two multicenter studies.