Acute symptomatic infection with Giardia duodenalis impairs iron absorption, but iron deficiency may protect against infections caused by various micro-organisms including parasites. We therefore examined the association of G. duodenalis infection and iron deficiency in 575 Rwandan children under 5 years of age. Giardia duodenalis infection was diagnosed by triplicate microscopy and PCR assays, and iron deficiency was defined as a ferritin concentration <12 ng/ml. Largely asymptomatic G. duodenalis infection was seen in 65.3% of the children and iron deficiency in 17.4%. G. duodenalis infection was less common in iron-deficient children (51%) than in non-deficient children (68%, P = 0.002). In multivariate analysis, the odds of G. duodenalis infection were almost halved in iron-deficient children (adjusted odds ratio, 0.54; 95% confidence interval, 0.33-0.86). In this highly endemic setting, there was no evidence that Giardia infection impairs iron status. Rather, iron deficiency appeared to protect against infection with this parasite.