Objective  Gonadal karyotyping is considered a tool for increasing our knowledge of disturbed gonadal development in patients with gonadal dysgenesis and for estimating more accurately the risk for gonadoblastoma formation. The objective was to gain insight into the role of Y chromosome distribution in the histological heterogeneity of gonads of patients with gonadal dysgenesis.

Design  Investigation of the possible relationship between peripheral blood karyotype, gonadal karyotype, morphological differentiation patterns of dysgenetic gonads and tumour formation.

Patients  In total 22 gonadal samples from 19 patients with gonadal dysgenesis (45,X/46,XY and variants n = 14; 46,XY: n = 3; 46,XX: n = 2) were examined.

Measurements  Morphological examination and immunohistochemical staining for testis specific protein, Y encoded (TSPY) and fluorescent and nonfluorescent in situ hybridization directly on gonadal tissue.

Results  No correlation was observed between peripheral blood karyotype and gonadal karyotype or between gonadal karyotype and the corresponding differentiation pattern. A Y‐containing cell line in Sertoli cells was encountered no more frequently than were other cell types.

Conclusions  The distribution of the Y‐containing cell line in peripheral blood is not a suitable indicator for predicting the histological differentiation pattern found in the gonads of patients with gonadal dysgenesis. The analysis of Y‐containing cell lines in the gonads of such patients could be informative with regard to the specific characteristics of gonadal development in humans as compared to chimeric mouse models. Moreover, it is essential to understand the mechanisms underlying disturbed gonadogenesis in these patients. As the gonadal karyotype is not related to the encountered gonadal differentiation pattern, it does not allow prediction of the risk for gonadoblastoma formation.