California is the leading producer of processing tomatoes, representing 96 and similar to 50% of USA and global production, respectively. All the processing tomato fields in the state are propagated by tomato seedlings produced at transplant nurseries. In this study, we implemented a hazard analysis of critical control points (HACCP) to identify, evaluate and propose management strategies to minimize plant pathogen infection risks across the tomato-seedling production system in three commercial transplant houses in California. To evaluate efficacy of sanitation practices we estimated microbial loads on trays and benches pre and post treatment and tested potting media and water as potential pathogen sources. Across all three facilities, propagation trays had high bacterial loads (>250 colony forming units 5 cm(-2)) after steam sterilization (82 degrees C). Bench disinfestation methods (application of sanitizing solutions) were ineffective in reducing microbial loads (bacteria and fungi). There was a high prevalence of standing water on the ground, in close proximity (15 cm) from the raised propagation benches, increasing the risk of water-splashed contamination with soil-borne pathogens. Media also contained high microbial (bacterial and fungal) loads. Both a Botrytis sp. (leaf blight) and Thielaviopsis basicola (black root rot) were recovered from symptomatic seedlings at high frequency, despite a rigorous fungicide regime, suggesting potential development of fungicide resistance. This study produces baseline information to develop a systems approach for managing pathogens at commercial tomato transplant nurseries.