Two studies of second graders at risk for reading disability, which were guided by levels of language & functional reading system theory, focused on reading comprehension in this population. In Study 1 (n = 96), confirmatory factor analysis of five comprehension measures loaded on one factor in both fall and spring of second grade. Phonological decoding predicted accuracy of real-word reading; automatic letter naming predicted rate of real-word reading; accuracy & rate of both real-word reading (more so than decoding of pseudowords) & text reading predicted reading comprehension & Verbal IQ also predicted reading comprehension. In Study 2 (n = 98), the treatment group (before/after school clubs receiving an integrated instructional approach that was supplementary to the general reading program) improved significantly more in phonological decoding & state standards for reading fluency than the control group (general reading program that had some code instruction but emphasized comprehension). The rate of phonological decoding explained 60.3% of real-word reading. Both treatment and control children improved significantly in reading comprehension, but controlling for pretreatment individual differences in oral vocabulary or in phonological decoding eliminated this effect. Taken together, the results of the two studies support two paths to reading comprehension: one from vocabulary & verbal reasoning, & one from written language that has multiple links between subskills: (a) alphabetic principle -> phonological decoding, (b) automatic phonological decoding -> accurate real-word reading, (c) automatic letter coding -> automatic word reading & (d) automatic word reading -> fluent text reading. Instructional implications of both paths & the links within the written language are discussed.