We present results of the study to identify gonosomal mosaicism and examine its inter-tissue variability in peripheral blood lymphocytes, buccal epithelium, and gonadal tissue in patients with disorders of sex development (DSD) associated with sex chromosome abnormalities (gonosomal DSD, n = 8) and gonad differentiation anomalies (46,XY DSD, n = 10). The study used a set of methods for analyzing individual cells: karyotyping and interphase FISH. According to the study results, gonosomal mosaicism was detected in 12 (67%) of the 18 examined patients. Cryptic, isolated by gonadal tissue, somatic mosaicism with 45,X cell line was detected in 4/10 46,XY DSD group patients. True inter-tissue mosaicism with two cell lines, one of which 45,X, was detected in 8/8 gonosomal DSD group patients. We propose using a new approach for mosaicism examination and quantifying mosaic cell lines variability. For this purpose, the coefficient of variation (CV) was used, the range of detected values was from 2.3 to 49%. In accordance with the obtained CV values, the inter-tissue variability was estimated as low, moderate or high. The correlation analysis revealed a statistically significant (p < 0.1) inverse correlation between Prader's stage and 45,X cell line percentage in lymphocytes, buccal epithelium, and gonadal tissue, as well as a direct correlation between the 45,X cell line presence in one of the tissues and its presence in other tissues. The search for mosaicism in tissues of different histogenesis origin using a set of methods for analyzing individual cells allows us to get a more complete picture of the gonosomal constitution and reveal a hidden imbalance, which is very important in examining patients with DSD. We proposed and used in this study the coefficient of variation (CV), which is a convenient statistical metric for quantifying the variability of cell lines in different tissues of a single patient and a step towards standardizing the results of genetic studies.