This study investigates the effectiveness of teacher instructions in academic reading lessons in two first-year classes at a university. A multiple case study design and the qualitative approach were applied to take an in-depth investigation into the problem. Five observations with a recorder and two observation schemes, one of which is based on the discourse analysis theory by Fairclough and the other is based on the theory of effective instructions, were conducted in each class to discover the way the teachers guided the students with the reading exercises. Moreover, the teachers’ and students’ perceptions of the effectiveness of the instruction given were measured by their responses in the interviews after the observation process. The data collected were coded and then decoded and analyzed under each research question. It was found out from the study that simple English words and structures were used in almost all the instructions. Moreover, both the teachers and the students were satisfied with the explicitness of the instructions. However, it is recommended that teacher instruction should still be improved. More referential questions should be used to catch the students’ attention and motivate them to think. More explanation and checking, including understanding checking and result checking, should be conducted to make sure the effectiveness of the instructions. The teachers also need to pay more attention to the guidance about how to deal with the questions and the language in the reading texts, as well.