Although the immune functions of insects are known to correlate with body condition and food resources, the association between habitat structure and immune function is still largely unknown. We studied the effects of forest clear-cutting on encapsulation rate in gynes and workers in the forest-dwelling ant Formica aquilonia. Forest logging resulted in disturbed immunity in workers and gynes. Logging enhanced encapsulation reaction in gynes, whereas decreased that of workers. In gynes, there was a likely trade-off between growth and immune function that was apparent in terms of different investment in size and immune function in different habitats. In workers, however, such associations were not found. The results indicate that, because of disturbed immunity, environmental stress may increase susceptibility of wood ants to diseases and parasites in disturbed habitats.