CD4+ T cells play a key role in the immune response of pathogen-induced mastitis in dairy cattle. Mammary gland factor STAT5b is involved in the regulation of CD4+T cell differentiation during inflammatory response and milk production. Little is known about the genetic variation effects of bovine CD4 and STAT5b genes on somatic cell score (SCS) and milk production traits in dairy cattle. The aim of the study was to investigate the single nucleotide polymorphisms (SNPs) of bovine CD4 and STAT5b in Chinese Holsteins and to analyse their association with estimated breeding values (EBVs) for SCS and milk production traits. In the present study, SNPs of CD4 (NC_007303 g.13598C>T) and STAT5b (NC_007317 g.31562 T>C) were identified and genotyped in Chinese Holstein population. The results showed that both SNPs were significantly associated with the EBVs for milk yield and protein yield in Chinese Holstein cows, and the SNP in CD4 was associated with the EBV for SCS (P<0·01). The additive effect of CD4 SNP on protein yield was significant (P<0·05), and the dominant effect of STAT5b SNP was significant on milk yield and protein yield (P<0·01). Cows with combination genotype C7 (CCTT: CD4 g.13598C>T and STAT5b g.31562 T>C) had the highest SCS EBV but lower milk yield, while cows with C2 (TTTC) produced more milk, fat and protein than the other eight combination genotypes. These results suggested that the SNPs in CD4 and STAT5b may be potential genetic markers for SCS and milk/protein yields selecting and warrant further functional research.