Production of pathogen-free plants can be subverted by organisms that are present in low numbers, have a latent phase, are systemic, or are difficult to detect because of equivocal symptoms. Agrobacterium tumefaciens and pathogenic Rhodococcus regularly defeat stringent sanitation and clean plant protocols, as will be illustrated using case studies from the Oregon State University Plant Clinic. Pathogen biology, gaps in knowledge, and human failings contribute to ongoing disease problems.