This study evaluated how predictive the California Mastitis Test (CMT) is for sub-clinical mastitis under tropical smallholder dairy production conditions in Kenya. It intended to establish whether the CMT usage could be contributing to misdiagnosis and consequent mistreatment with animal drugs resulting in residue problems. Milk samples (n = 239) were aseptically collected from lactating cows in the Rift Valley of Kenya and tested using the CMT, somatic cell counts (SCC) and bacterial culture. The samples were also screened for violative drug residues using the commercial delvo test and compared to the milks mastitic status for possible association. There was a numerical but non-significant (p > 0.05) difference evident in the frequencies observed using the three different mastitis indicators. The prevalent bacterial species isolated from mammary glands with subclinical mastitis were Staphylococcus aureus (45.6%), coagulase-negative Staphylococci (13.0%), Streptococci (11.7%) and Escherichia coli 5.9%. There was an overall poor but significant (p < 0.05) correlation between the CMT and the violative antimicrobial residues in samples from all quarters, infected and non-infected respectively. The results suggest that the CMT use amongst the smallholder dairy sector as a mastitic indicator may not be a risk factor in violative antimicrobial residues problems in milk.