The initiatives in U.S. school reform constantly serve as a reflection of the academic, political, and economical sentiment of the time. The College Entrance Exam Board’s decision in 1909 to establish a 40 to 60 minute class schedule that mirrored the Carnegie unit’s structure of efficiency and mass production remained the tradition until 1959, when J. Lloyd Trump introduced a flexible instructional schedule that allotted for an 85 to 100 minute “block” of time for each subject. The government report, A Nation at Risk (1983), found that 13% of seventeen year olds were functionally illiterate, and that schools were not utilizing school time efficiently. By 2001, the No Child Left Behind Act established a structured accountability system for schools; however, by 2013, the National Center for Educational Statistics (2013) reported five year stagnation in reading performance for fourth, eighth, and twelfth graders. The current outcomes have caused administrators and educators to revisit current instructional and organizational practices for more efficient and effective approaches to maximize learning opportunities and increase school performance. This study examined the effects of implementing a balanced literacy approach to reading in self-contained and departmentalized classrooms in second grade classrooms. In a review of the literature, little research has been conducted on self-contained and departmentalized classroom settings in the elementary school prior to third grade. Previous studies primarily focused on students in third grade and higher, and concentrated on student performance on state-mandated tests in reading. No studies to date have investigated self-contained and departmentalized comprehension levels prior to a grade level that has been designated for a state-mandated test. As a result, this study examined the following research questions: 1) What effect does receiving balanced literacy instruction in a self-contained or departmentalized classroom have on the reading comprehension of second graders as measured by district assessments, and 2) Are there gender differences in the observed reading comprehension of second graders with regard to a self-contained or departmentalized classroom? The research also qualitatively examines what effect teachers’ experiences, perceptions, and opinions about self-contained and departmentalized instruction have on the implementation and academic outcomes of the instructional organization of the classroom. This study examined second grade students from an urban school district in a metropolitan area in Texas. The sample was taken from three self-contained second grade classrooms (N = 61) and four departmentalized second grade classrooms (N = 86) from the same elementary campus. The departmentalized classrooms served as the quasi-experimental group and the self-contained classrooms served as the control group. Statistical tests were conducted to answer the first two research questions. Repeated measures were administered to compare beginning middle, and end of year comprehension levels within each group to determine significant progress. A 2 x 2 x 3 mixed ANOVA was used on the subpopulation (gender) to determine if any gender differences exist. Individual interviews of the second grade teachers that participated in the study were conducted to collect feedback regarding teachers’ beliefs, opinions, and preparation for self-contained and departmentalized literacy instruction. Results from separate analyses of the comprehension levels indicated that both the departmentalized and self-contained groups made significant progress from the beginning to the middle of the school year, and again at the end of school year. However, there was no significant difference in the rate of increase in self-contained and departmentalized groups. Significant progress was also made for each group within the gender subpopulation. When the departmentalized and self-contained groups were compared, there was not a significant difference between the comprehension levels of males and females at the end of the year. There was also no significant difference in the rate of increase in comprehension levels of departmentalized and self-contained males, and the rate of increase in comprehension levels of departmentalized and self-contained females at the end of the year. Feedback from teachers revealed that all of them supported the opportunity for more preparation and focus on one subject. However, self-contained teachers preferred the opportunities to teach one theme across all subjects, while departmentalized teachers preferred opportunities to engage in more cooperative learning activities during the literacy block. This study demonstrates that balanced literacy instruction is effective in increasing student comprehension levels from the beginning to the end of the school year in primary classrooms that implement both a departmentalized and self-contained schedule. It also demonstrates that departmentalized and self-contained balanced literacy can also increase student comprehension levels from the beginning to the end of the year within both gender groups.