Histopathological and spermatogenesis classification by Johnsen is widely used in the germinal epithelium maturation analysis, besides identifying pathological alterations able to cause subfertility and even infertility. The aim of this study was to analyze cell-differentiation histopathological data and to correlate them with expression of PRM-1, TNP-2, 17β-HSD3, LHR, generic MHC-I, MIC-B, NC1 and NC3 genes, involved in bovine spermatogenesis using qRT-PCR from testicular parenchyma. Based on Johnsen’s criteria, the results showed normal spermatogenic activity in these animals, classified at 6, 7 and 8 scores. The qRT-PCR analysis expression showed that MHC-I (generic) gene was less expressed than all the other genes in evaluated scores (p < 0.05) and, PRM-1 and TNP-2 were the most expressed genes (p < 0.05). The PRM-1 gene expression was significantly higher than TNP-2 (p < 0.05). Comparing scores, 17β-HSD3 gene expression was lower (p < 0.05) in score 6 when compared to scores 7 and 8 animals. It was also observed that PRM-1 expression was lower in score 6 when compared to 7, as well as TNP-2 gene was less expressed in the score 6 (p < 0.05) when compared to 7 and 8 scores. Our results demonstrated that MHC I (generic), MIC-B, NC1, NC3, and LHR genes are poorly expressed in bovine testis, suggesting their marginal action on spermatogenesis. Instead, PRM-1, TNP-2, and 17β-HSD3 expression were higher, supporting the notion that these genes can act directly on the germ cells differential development during bovine spermatogenesis.