Genetic diversity is vital for species’ adaptation to environmental changes, including disease pressures. Parasites exert strong selective forces, often linking reduced genetic diversity with increased infection susceptibility. However, the impact of genetic diversity at both functional and neutral loci on infection patterns in natural populations remains unclear. This meta-analysis examines the relationship between genetic diversity and protozoan infections across multiple avian species, focusing on genetic marker type (functional vs. neutral), parasite genus, and host migratory behaviour. Data from 29 studies covering 24 bird species and 72 effect sizes—derived from a variety of genetic markers and infection metrics (prevalence and intensity)—were synthesized. Contrary to expectations, no significant relationship was found between individual genetic diversity and infection prevalence or intensity, regardless of marker type. Meta-regression analyses revealed that neither parasite genus nor migratory behaviour altered the association between genetic diversity and infection measures. Our findings do not support the notion that host genetic diversity shapes infection patterns within populations. However, broad genetic diversity measures may obscure finer genetic effects from specific alleles (e.g., MHC variants), and reliance on parasite genetic material alone may underrepresent infection status. Future studies should integrate broad genetic diversity measures with allele-specific analyses and include antibody testing to better assess infection history, offering a fuller view of host-parasite co-evolution in natural ecosystems.