While it is known that document design affects the reading process (Schriver, 1997), there are few studies on how designelements influence non-native readers’ reading. We conducted a study to examine how native and non-native (NN) readersread Japanese web documents with different structures (networked, hierarchical, and relational) using eye-tracking andhow differences in reading affect information lookup and comprehension evaluated by performance and comprehensiontests. We used municipal documents currently made available on the Web by local governments in Japan. Seven nativeand eight NN Japanese readers took part in the study. The results show that native readers are not influenced by differencesin document structure. NN readers, on the other hand, showed different patterns of reading depending on the documentstructure, and better information look up performance when they read documents with a relational structure. This seemsto be related to the amount of information available.