This paper aims to fill the research gap of Generations Y and Z customer preferences in Czech and Slovak Republic market, by identifying the factors determining the purchase of organic food. The research focused on the price influence, trustiness of organic food quality, health impact of organic food, brand motivation and place of purchase preferences. The primary data were collected through two identical survey cycles. The first one was carried among the Generation Y respondents in 2014, the second one among the Generation Z respondents in 2019. Both the survey cycles were distributed in electronically among 1708 respondents in total. The relative frequency testing was used to process the questionnaire data, the hypothesis verification was tested by one variable and two variable tests of frequencies. To analyse the generation Z respondents´ purchase factors relations, the logit model was used. As independent variables were set the factors determining the purchase, as dependent variable was set the realisation of purchase of organic products. The results show that the popularity of organic food is higher for the generation Z than for generation Y. The appearance factor of the organic products does not influence the decision of the Y generation about buying the product, but the factors of availability and quality factors influence the decision the most. The factors determining organic food preferences can allow company management to establish reliable marketing communication and sale strategy tailored to the generation Y and Z customer segment in Central Easter Europe.