The aim of this study was to investigate effects of kefir, a traditional source of probiotic, on coccidial oocysts excretion and on the performance of dairy goat kids following weaning. Twin kids were randomly allocated to one of two groups at weaning. Kids of the first group received 20 ml of kefir daily for 6 weeks (KEF), while kids in the control group were given a placebo (CON). Individual faecal samples were regularly ( = 18 per kid) taken to quantify the number of coccidial oocysts per gram of faeces (OpG). There were no differences between the groups in terms of body weight development ( > 0.05) and feed consumption. Kids of both groups were not able to consume enough feed to meet their nutrient requirements during the first 3 weeks following weaning. KEF had a lower frequency of OpG positive samples than CON ( = 0.043). Kefir did not affect the maximum oocyst excretion and age of the kids at the highest oocyst excretion ( > 0.05). KEF shed numerically 35% lower coccidial oocysts than the controls, which corresponded to a statistical tendency ( = 0.074) in lowering Log-OpG in comparison to CON. While KEF had a lower frequency of OpG positive samples and tended to shed lower OPG by around one-third, the frequency of diarrhea, level of highest oocyst excretion, and performance of the kids remained unaffected. Therefore, it is concluded that overall effects of kefir do not have a significant impact on sub-clinical infection and performance in weaned kids under relatively high-hygienic farming conditions.