We assessed adherence in an infant tuberculosis prevention trial in Kenya with a urine isoniazid metabolite-detecting dipstick. Ninety-seven infants had 155 assays performed; 77 (49.7%) were found to be positive despite caregiver-reported adherence. Positive assays were associated with maternal secondary education, HIV suppression and no reported missed doses in past 3 days, suggesting caregiver education and self-medication use influenced infant adherence.