Color defines one aspect of quality for tomato and tomato products. Carotenoid pigments are responsible for the red and orange colors of tomato fruit, and thus color is also of dietary interest. The aims of this study were (1) to determine the relative importance of field sampling and analytical replication when measuring lycopene and beta-carotene in tomato fruit and (2) to determine the effect of yellow shoulder disorder (YSD) on the content of lycopene and beta-carotene in tomato juice and tissue. Our results show that increasing biological replications is an efficient strategy for reducing the experimental error associated with measurements of lycopene and beta-carotene. Analytical replications did not contribute significantly to observed variation, and therefore experimental efficiency will be gained by reducing analytical replications while increasing field replication. We found that YSD significantly reduces lycopene in affected tissue and in juice made from affected fruit. In contrast, beta-carotene concentrations were only reduced in affected tissue but were not significantly reduced in juice. With increasing interest in biofortified crops, modulating the carotenoid profile in tomato by minimizing YSD symptoms represents a strategy for improving tomato fruit quality that is currently supported by grower contract structure and processor grades.