<p>Migratory birds are exposed to a diverse fauna of parasites and vectors throughout their annual cycle, which can potentially facilitate disease transmission across wide geographic ranges. However, few studies have examined how these pathogenic organisms affect the immune profiles and body condition of avian hosts while they are refueling at stopover sites. Here, we used molecular barcoding and microscopic examination to detect, quantify, and identify haemosporidian parasites in Chilean Elaenias (<i>Elaenia chilensis</i>) during their migration stopover in the Serra do Mar, Brazil. We then evaluated whether haemosporidian infections were associated with immunological condition (heterophil, lymphocyte, and H/L ratios), body condition, and fat storage. Among the 79 adult Chilean Elaenias captured, 26 were infected with haemosporidian parasites. However, most individuals carried extremely low parasite burdens during migration. Contrary to our expectations, haemosporidian infection did not affect body condition or fat storage in migrating Chilean Elaenias, regardless of host sex. Likewise, the absence of a relationship between immunological parameters and parasite presence suggests that haemosporidian parasitism does not significantly impact the immune response of these migrating birds. Moreover, the condition of chronically infected and uninfected Chilean Elaenias did not differ, suggesting that these parasites may not constrain host arrival at the stopover site in Serra do Mar.</p>