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Porous cranial lesions (cribra cranii and cribra orbitalia) are widely used by archaeologists as skeletal markers of poor child health. However, their use has not been validated with systematic data from contemporary populations, where there has been little evidence of these lesions or their health relevance. Using 375 in vivo computed tomography scans from a cohort-representative sample of adults aged 40+ years from the Bolivian Amazon, among food-limited, high-mortality forager-farmers, we identified cribra cranii on 46 (12.3%) and cribra orbitalia on 23 (6%). Cribra orbitalia was associated with several hallmarks of compromised immune function, including fewer B cells, fewer naïve CD4⁺T cells, a lower CD4⁺/CD8⁺T cell ratio, and higher tuberculosis risk. However, neither lesion type predicted other physician-diagnosed respiratory diseases, other markers of cell-mediated immunity, or hemoglobin values. While cribra orbitalia shows promise as a skeletal indicator of health challenges, our findings do not support the continued practice of using these lesions to infer anemia in adults.