This study describes a non-adult individual with bone features suggestive of β-thalassemia, a disease commonly found in malaria-endemic regions today and in the past. The skeleton of a 5.5-to 6.5-year-old child exhumed from a 16th-to 18th-century CE necropolis in Almeirim (Portugal) was examined macroscopically, with a scanning electron microscope, and by conventional radiology and computed tomography. This individual shows frontoparietal diploic hyperplasia with a slight hair-onend radiographic appearance and an exuberant serpiginous pattern. The orbital roofs have a plaque-like formation and facial bones display new bone proliferation and porosity. The teeth show caries, calculus deposition, anomalies on the four deciduous canine roots, and linear enamel hypoplasia on the first permanent right upper central incisor. The postcranial skeleton presents osteopenic trabecular appearances, cribra humeralis, and cribra femoralis, the latter associated with malaria. A second non-adult individual (2.5-3.5 years old) had similar lesions in the cranium, raising the question of whether they were siblings. The lesions are consistent with β-thalassemia intermedia, a homozygous or compound heterozygous hemoglobinopathy found in malaria-endemic regions, such as Almeirim, due to the protective advantage conferred by β-thalassemia carriers. Thalassemia presents a wide spectrum of lesions common in other hemolytic anemias, which makes the diagnosis a challenge. Hopefully, biomolecular techniques will assist the diagnosis in skeletonized individuals. To the authors' knowledge, this is the first possible case of thalassemia in the westernmost part of Europe, in a region currently with high prevalence of hemoglobinopathies, attributed to the past Islamic and sub-Saharan presence, and in an area historically affected by malaria.