This study investigated the relationship of student-generated questions and prior knowledge with reading comprehension. A questioning hierarchy was developed to describe the extent to which student-generated questions seek different levels of conceptual understanding. Third- and fourth-grade students (N = 360) posed questions that were related to their prior knowledge and reading comprehension, measured as conceptual knowledge built from text. The results indicated that student questioning accounted for a significant amount of variance in students' reading comprehension, after accounting for the contribution of prior knowledge. 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.