In the field of reading comprehension, student-generated questions have been investigated within instructional contexts for elementary, middle school, high school, and college students. Although findings from instructional studies reveal that student-generated questions have an impact on reading comprehension, past research has not examined why student-generated questions improve text comprehension. This study investigated the relationship of student-generated questions and prior knowledge to reading comprehension by examining the characteristics of student-generated questions in relation to text. A Questioning Hierarchy was developed to examine the extent that questions elicit different levels of conceptual understanding. The questions of third- and fourth-grade students (N= 208) about expository texts in the domain of ecological science were related to students' prior knowledge and reading comprehension. Reading comprehension was measured as conceptual knowledge built from text and by a standardized reading test. As hypothesized, questioning accounted for a significant amount of variance in students' reading comprehension after the contribution of prior knowledge was accounted for. Furthermore, low- and high-level questions were differentially associated with low and high levels of conceptual knowledge gained from text, showing a clear alignment between questioning levels and reading comprehension levels. Empirical evidence showed that conceptual levels of students' questions were commensurate with conceptual levels of their reading comprehension. This alignment provides the basis for a theoretical explanation of the relationship between reading comprehension and the quality of student questioning.