Consumers are increasingly becoming very concerned about food safety, with many giving preference to organic food products over conventional food products, which make use of agrochemicals with potential implications for health. Furthermore, to make the food choice decisions even more complex, genetically modified (GM) foods have been introduced in an attempt to meet global food demand. Consumers therefore must make decisions regarding organic and GM foods. This paper investigates consumer heterogeneity for organic and GM tomatoes in Ghana using advanced discrete choice modelling techniques. The data for empirical application come from a choice experimental study conducted among 200 consumers in Ghana. Our econometric modelling revealed that the sampled consumers preferred organic tomatoes that are produced locally and certified by the Food and Drugs Authority. However, we find a likelihood that women and older consumers may have preferences for GM tomatoes with environmental and health benefits. Policy implications are drawn from the findings of the study