Purpose The main aim of this study was to investigate the contribution of aspects of vocabulary, word reading abilities, and reading experience to reading comprehension, and to analyse sub-samples of students with comprehension difficulties. Method The study employed a cross-sectional design. Full data sets were obtained from 179 Danish Grade 3 pupils. Participants were given a standard reading comprehension test requiring multiple-choice answers to six different texts of various length and type. Orthographic and phonological coding, as well as non-verbal problem solving were assessed by means of standard tests. Assessments of reading experience and aspects of vocabulary (size and semantic lexical structuring) entailed new assessment tools developed for group administration by the authors of this paper. Lexical structuring was assessed with odd one out tasks (e.g. which one does not belong here: path, street, road, river). Results Data analyses showed that in the entire sample, skills of semantic lexical structuring and reading experience made strong contributions to reading comprehension. Analyses of the pupils below the 25%-percentile in reading comprehension revealed that for the vast majority simultaneous phonological and orthographic coding difficulties were found as well. Conclusions The results suggest that access to semantic structuring of lexical items play an important role in reading comprehension abilities for the entire group of 3rd graders. However, for those with poor comprehension basic word reading abilities still made the most constraints on their comprehension. The results are discussed in the light of Ricketts et al. (2008) and Perfetti & Hart (2002).