Academic reading and writing abilities are prerequisites for success in postgraduate programmes. These are particularly important domains of competence for students in applied linguistics, whose studies and future performance require insight into these skills. A validated self-assessment questionnaire was administered to 194 graduate students of applied linguistics, who assessed their own academic reading skills. In addition, open-ended questions added to the questionnaire and interviews with 14 students were analyzed, yielding eight domains identified as particular challenges. The results revealed that students assessed their information literacy to be the weakest domain. The eight areas of challenge included: shortage of time, information literacy, content knowledge, critical literacy, writers' language styles and generic features of texts, teachers' high expectations and vague instructions, insufficient statistical literacy and insufficient interaction with peers. The implications for English for Academic Purposes (EAP) instruction are discussed.