Parasites are ubiquitous in wild animals, with host-specific life histories considered as major determinants of prevalence and parasite assemblage patterns. It is predicted that habitat differences in logged rain forests influence population performances of small mammals and consequently may change the infection patterns of local animal populations with regard to endo- and ectoparasites. We investigated patterns of helminth species assemblages (Nematoda, Platyhelminthes) in two rat species (Leopoldamys sabanus, Niviventer cremoriventer) and two tree shrew species (Tupaia tana, T. longipes) in three logged and three unlogged rain forests in Borneo by examining 337 faecal samples with non-invasive faecal egg count (FEC). Nematode eggs prevailed in 95% of all samples with up to five (mean 1.9 ± 1.1) morphotypes. Whereas members of Strongylida were most prevalent in L. sabanus, T. tana and T. longipes, Spirurida dominated in N. cremoriventer that revealed at the same time the lowest average nematode prevalence and FEC. Cestode eggs were only found in L. sabanus and T. tana. Composition and abundance patterns of the parasitic helminth assemblages were influenced by logging. As hypothesized, species richness of nematode morphotypes and mean number of infections per host of T. longipes were larger in logged than in unlogged forest. In contrast, L. sabanus was more heavily infected with cestodes in unlogged than in logged forest and also revealed larger egg counts for strongylids and spirurids in unlogged forest. Our results suggest that forest degradation and altered environmental conditions influence helminth diversity and infection patterns of small mammals with contrasting trends among host species. The inconsistent logging-induced changes in helminth assemblages from different hosts indicate that specific sets of habitat-host-parasite interactions are uniquely influenced by the effects of logging. Consequently, predictions on changes of parasite diversity and prevalence with regard to habitat disturbance need to be based on the individual life histories of the hosts (and the parasites).