In political science, data with heterogeneous units are used in many studies, such as those involving legislative proposals in different policy areas, electoral choices by different types of voters, and government formation in varying party systems. To disentangle decision-making mechanisms by units, traditional discrete choice models focus exclusively on the conditional mean and ignore the heterogeneous effects within a population. This paper proposes a conditional binary quantile model that goes beyond this limitation to analyze discrete response data with varying alternative-specific features. This model offers an in-depth understanding of the relationship between the explanatory and response variables. Compared to conditional mean-based models, the conditional binary quantile model relies on weak distributional assumptions and is more robust to distributional misspecification. The model also relaxes the assumption of the independence of irrelevant alternatives, which is often violated in practice. The method is applied to a range of political studies to show the heterogeneous effects of explanatory variables across the conditional distribution. Substantive interpretations from counterfactual scenarios are used to illustrate how the conditional binary quantile model captures unobserved heterogeneity, which extant models fail to do. The results point to the risk of averaging out the heterogeneous effects across units by conditional mean-based models.