To present a case of premature ovarian failure (POF) and a complex chromosomal rearrangement involving band Xq21.Case report.Department of cytogenetics, general analysis laboratory.A woman with POF and a complex translocation involving chromosomes X and 2 and a nucleolus organizer region (NOR) structure inserted in the critical region Xq21.Chromosomal analysis, NOR banding, hysteroscopy.Fluorescence in situ hybridization, comparative genome hybridization, human androgen receptor gene technique.Four mechanisms may explain a causal relationship between the phenotype of the patient and her chromosome constitution. The presence of a NOR structure at the breakpoint of chromosome X suggests a complex reorganization and is of interest per se.Cytogenetic analysis is essential in women with unexplained POF and may provide valuable information on the chromosome location of critical regions implicated in ovarian function. However, in very complex reorganizations such as that described herein, classical cytogenetic techniques must be combined with molecular techniques to achieve a more complete characterization of the anomaly.