SRY on the Y-chromosome acts as a transcription factor to initiate testicular differentiation in mammals. Sox9 is a SRY target gene, upregulated immediately after Sry expression, and plays a key role in testicular differentiation. In the present study, we examined the expression of SRY and SOX9 proteins in the B6.Y(TIR) gonad, which undergoes partial or complete sex reversal. The results show that the ontogeny of SRY expression in the B6.Y(TIR) gonad was comparable with that in the B6.XY gonad. On the other hand, while SOX9 expression immediately followed SRY expression in the B6.XY gonad, it was considerably delayed compared to SRY expression in the B6.Y(TIR) gonad or SOX9 expression in the B6.XY gonad. Although SOX9 expression reached the entire gonad at a time point, it was downregulated and became restricted to the central area in which testis cords were organized. MIS, a marker of Sertoli cells, appeared only in well-organized testis cords. We speculate that the SRY protein from the Y(TIR)-chromosome is inefficient in upregulating the Sox9 gene on the B6 background, allowing the initiation of ovarian differentiation.