The present article reports a case of Whipple's disease as a rare cause of intestinal malabsorption syndrome, in a young individual with G6PD deficiency and hypothyroidism, without previous follow-up. The male patient initially complained of diarrhea and long-standing weight loss. The complementary examination findings were consistent with Whipple's Disease. Antibiotic therapy (Ceftriaxone) was initiated with subsequent clinical improvement. Although rare, this disease should be considered as a differential diagnosis in patients with intestinal malabsorption, especially considering the systemic impact of the disease and the possible control with appropriate antibiotic therapy.