A key determinant of children's health is the quality and quantity of their food and energy intake. In middle childhood children gain greater independence over their food choices. Understanding the factors that influence their choices is therefore important, particularly in the context of obesogenic food environments where children need to learn to identify and select healthier options. This study aimed to examine the role of food attributes in affecting children's food preferences and perception of healthiness and tastiness. A secondary aim was to determine if portion size was related to children's food perceptions and preferences. Participants (children 5–12 years) completed a discrete choice experiment (n = 2112) that examined their perceptions of bread and smoothies when the attributes of type/flavour, food form and portion size were systematically varied. Children were asked about their (i) food preferences, and their perceptions of (ii) healthiness and (iii) tastiness. Data were analyzed using a conditional logit model for the foods independently, and the relative contribution of the attributes to children's preferences, and perceptions of healthiness and tastiness was determined. The results found that children primarily used the type/flavour of the breads and smoothies to form their preferences and perceptions, and the other attributes (portion size and food form), had minimal influence. This study found that children aged 5–12 years made simple food choices and formed perceptions of how healthy or tasty a food was based on a single food characteristic (the type/flavour), ignoring the portion size and food form. This suggests that when children in middle childhood make food choices, they are likely to rely primarily on the food's flavour or type and do not consider other important attributes that will affect their diet quality and energy balance.