Parasite infection in young animals can affect host traits related to demographic processes such as survival and reproduction, and is therefore crucial to population viability. However, variation in infection among juvenile hosts is poorly understood. Experimental studies have indicated that effects of parasitism can vary with host sex, hatching order and hatch date, yet it remains unclear whether this is linked to differences in parasite burdens. We quantified gastrointestinal nematode burdens of wild juvenile European shags (Phalacrocorax aristotelis) using two in situ measures (endoscopy of live birds and necropsy of birds that died naturally) and one non-invasive proxy measure (fecal egg counts (FECs)). In situ methods revealed that almost all chicks were infected (98%), that infections established at an early age and that older chicks hosted more worms, but FECs underestimated prevalence. We found no strong evidence that burdens differed with host sex, rank or hatch date. Heavier chicks had higher burdens, demonstrating that the relationship between burdens and their costs is not straightforward. In situ measures of infection are therefore a valuable tool in building our understanding of the role that parasites play in the dynamics of structured natural populations.