Salmonella contamination associated with market fresh tomatoes has been problematic for the industry and consumers. A number of outbreaks have occurred, and dollar losses for the industry, including indirect collateral impact to agriculturally connected communities, have run into the hundreds of millions of dollars. This review covers these issues and an array of problems and potential solutions surrounding Salmonella contamination in tomatoes. Some other areas discussed include (i) the use of case-control studies and DNA fingerprinting to identify sources of contamination, (ii) the predilection for contamination based on Salmonella serovar and tomato cultivar, (iii) internalization, survival, and growth of Salmonella in or on tomatoes and the tomato plant, in biofilms, and in niches ancillary to tomato production and processing, (iv) the prevalence of Salmonella in tomatoes, especially in endogenous regions, and potential sources of contamination, and (v) effective and experimental means of decontaminating Salmonella from the surface and stem scar regions of the tomato. Future research should be directed in many of the areas discussed in this review, including determining and eliminating sources of contamination and targeting regions of the country where Salmonella is endemic and contamination is most likely to occur. Agriculturalists, horticulturalists, microbiologists, and epidemiologists may make the largest impact by working together to solve other unanswered questions regarding tomatoes and Salmonella contamination.