We conducted a cross-sectional study in northwest Mexico in order to investigate the association between giardiasis and serum vitamin A in 40 Giardia-infected and 70 Giardia-free schoolchildren who were covered by a regional school breakfast program. There were no significant differences in age, Z-scores for nutritional indices of height for age, weight for age, or weight for height, socioeconomic conditions (employment and education of the parents, household conditions, sanitation facilities, type of drinking water, and family income), and mean daily intakes of vitamin A in the Giardia-free (899 ± 887 μg) and the Giardia-infected (711 ± 433 μg) groups. A higher concentration of serum retinol was found in the Giardia-free group than in the Giardia-infected group (0.75 μmol/L versus 0.61 μmol/L, respectively; p < 0.0001). Giardia-infected children were more likely to be vitamin A-deficient than the Giardia-free children (OR = 3.2; 95% CI = 1.2–8.5). Although 95% of the children met the daily-recommended intakes of vitamin A, half of them showed subclinical vitamin A deficiency. It is recognized that vitamin A deficiency is multifactorial and giardiasis was a factor significantly associated with this deficiency in this study. Mexican program developers and policymakers should be aware about the distinction between dietary deficiencies and deficiency diseases when current national program strategies for parasitic control and vitamin A supplementation are redesigned.