The rapid rate of habitat loss in Madagascar urges a comprehensive assessment of the threats that its fauna faces by living in fragmented, secondary and/or exotic forests. The role of habitat disturbance in determining potential boosts of parasite infections in lemurs, for instance, has been only recently investigated. Here, we conducted a preliminary assessment of prevalence and intensity of gastrointestinal parasite infections in two populations of endangered red-collared brown lemurs, Eulemur collaris (Geoffroy, 1812) (Mammalia: Lemuridae), living in two littoral forest fragments of southeastern Madagascar. We collected faecal samples from 45 lemurs. The samples were stored in 70% alcohol, and we used a modified McMaster technique to analyze egg shedding. The analysis revealed only nematode infections. We found a higher prevalence of infection in the more disturbed fragment, while no differences were revealed in terms of infection intensity. Prevalence of infection was found to be sex-biased in the less degraded area, being higher in females. We hypothesize that this might have been caused by female immune suppression due to increased energetic costs during pregnancy and/or to avoid possible harm to the foetus. Since red-collared brown lemurs are the largest seed dispersers in the littoral forest and only small populations survive in a few fragments, the implications of our results should be considered in future conservation plans for this habitat.