This study explores the nature of reading comprehension difficulties among early adolescent language minority (LM) learners and native English speakers in urban schools. Sixth-grade students (399 LM learners, 182 native English speakers) were screened for difficulties, using a standardized measure of reading comprehension. Of these, 262 students (201 LM learners, 61 native English speakers) with a score at or below the 35th percentile were administered measures of oral language and reading. More LM learners than their peers were classified as struggling readers (60% vs. 40%, respectively). However, latent class analysis demonstrated that the two populations were evenly distributed among three skill profiles of struggling readers. Despite relative differences in word reading accuracy and fluency, each profile was characterized by low vocabulary knowledge. The majority of struggling readers were found to have developed basic fluency skills. The findings demonstrate the need for middle schools to identify why students are having comprehension difficulties and to target instruction to meet their specific needs, given the wide variation in the struggling reader population. Moreover, they suggest that treating LM learners as a separate group based on their status as second-language learners may not be appropriate. (Contains 4 tables, 1 figure and 6 notes.)