Heligmosomoides polygyrus is a gastrointestinal nematode whose adult distribution is restricted to the duodenal region in the small intestine of the mouse. This study tests the hypothesis that the habitat of these parasitic worms is influenced by fixed (architectural) cues in the small intestine of the vertebrate host, and that H. polygyrus adults will select microhabitats containing the longest villi. H. polygyrus adults attach by coiling around the villi, and longer villi may provide greater attachment resources. In addition, these parasites feed on the epithelial cells covering the villi and thus longer villi may also provide more food resources. Using histological methods, this study identified a gradient of villus length in the small intestine of the mouse where the longest villi were found in the duodenum and shortest in the ileum Several non-surgical and surgical treatments were used to differentially alter the overall lengths of the villi. These treatments produced a significant negative correlation between villus length and worm distribution, with the worms selecting regions with the relatively longest villi in the small intestine. Attachment and feeding sites are crucial resources for this parasite, and these data suggest that villus length may be a reliable indicator of resource quality, and that decisions on habitat suitability by H. polygyrus adults may depend on this single, topological variable.