Mercury can have profound and complicated effects on the immune system, and epidemiological evidence regarding the relationship between mercury exposure and allergic disorders has been sparse. We investigated the associations between mercury levels in maternal and children's hair and the risk of wheeze and eczema in Japanese children at 29-39 months of age. Study subjects were 582 Japanese mother-child pairs. Presence or absence of wheeze and eczema symptoms was determined based on the criteria of the International Study of Asthma and Allergies in Childhood. Adjustment was made for maternal age; residential municipality at baseline; maternal and paternal education; maternal and paternal history of allergic disorders; maternal energy-adjusted fish intake during pregnancy; maternal smoking during pregnancy; number of child's older siblings; child's sex; household smoking in the same room as the child; breastfeeding duration; and children's fish intake at the fourth survey. The prevalence of wheeze and eczema was 18.6% and 17.2%, respectively. The range of hair mercury levels was 0.26-6.05 μg/g in mothers and 0.13-9.51 μg/g in children. Neither maternal nor children's hair mercury levels were related to the risk of wheeze or eczema. Maternal and children's hair mercury levels in the second quartile were non-significantly inversely related to the risk of wheeze (adjusted odds ratios [95% confidence intervals] were 0.77 [0.41-1.44] and 0.57 [0.29-1.11], respectively) while those in the third quartile were non-significantly inversely associated with the risk of eczema (adjusted odds ratios [95% confidence intervals] were 0.77 [0.40-1.45] and 0.66 [0.33-1.30], respectively). The current study provides no evidence that hair mercury levels in either mothers or children are positively associated with the risk of wheeze or eczema in children aged 29-39 months in Japan, where fish intake is high.