Background This study describes the barriers to effective and timely LTBI treatment encountered in a research study on INH adherence in Latino adolescents. Method Participant study logs were reviewed, results of continuing medical education pretests for medical providers were examined, and participating medical facilities were contacted in order to construct a profile of multi-level barriers to LTBI treatment. Results A total of 285 TST positive Latino (96%) high school students were recruited into the trial. We encountered a lack of understanding of the gravity of tuberculosis infection among both the public and providers of health care. Parents and adolescents cited competing priorities, transportation problems and financial constraints as reasons for non-compliance. Discussion Improved education of the public and physicians is needed regarding the gravity of the disease and the value of treatment, as well as public and financial support for LTBI treatment by both the government and the medical community.