Objectives Turner syndrome (TS) is one of the most common chromosomal abnormalities with an incidence of approximately one in 2,500 live births. Short stature and primary ovarian insufficiency are two most important characteristic findings of TS. Turner syndrome karyotypes include monosomy X, mosaic structure and X chromosome structural anomalies. Genotypic and phenotypic characteristics vary among cases. This study aimed to evaluate the clinical variations observed in TS cases with the copy number variations (CNV) detected by microarray study. Methods Fifty-three patients diagnosed with TS, between the ages of 0–18 were included in the study. Peripheral blood samples were taken from 36 cases for microarray study. Results Karyotypes were as follows: thirty-three of cases were 45,X, 7 were 45,X/46,XX, 6 were 45,X/46,Xi(Xq), 2 were 46,Xi(Xq), 2 were 45,X/46,r(X), 1 was 45,X/46,Xi(Xp), 1 was 45,X/46,XY and 1 was 45,X/46,X+mar(idicY) karyotype. A significant correlation was found between karyotype groups and FSH values of the cases (p=0.034). In monosomy X and mosaic isochromosome Xq cases, the FSH value was found to be significantly higher than those with 45,X/46,XX mosaic karyotype. CNVs were found in 8 (22.2%) out of 36 cases whose microarray study was performed. Unexpected atypical findings were discussed in the light of the characteristics of CNVs. Conclusions In conclusion, the microarray method has a great contribution in explaining many unexpected findings in TS cases. Moreover, those CNV findings may contribute for the explanation of the underlying mechanisms of those anomalies.