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This is a great question. We have had some success using oral reading of passages with questions that range from simple facts to making inferences. There are also some maze (or cloze) tasks that can be used which are quick and informative. The dilemma, of course, is that comprehension relies on text difficulty, students’ background knowledge, and student motivation.

In Florida, the new state assessment FAIR, uses leveled passages that students read aloud. The accuracy and rate with which students read the passages is highly correlated with reading comprehension skills, particularly in the early grades. DIBELS passages, which use a similar format are also useful for monitoring fluency. Of course, there is more to comprehension that just rate and accuracy but the constructs are all related and so these fluency measures can be useful, when coupled with questions, to monitor fluency.

For more complex ways of assessing comprehension, and depending on the age of the students, Word Generation, developed by SERPS,  might provide some ideas for middle school students as well.

Response from RTI Action Network
Information is also provided in “Screening for Reading Problems in Grades 4 Through 12” by Evelyn S. Johnson, Ed.D., Juli Pool, Ph.D., and Deborah R. Carter, Ph.D.