We set out to study how anti-filarial IgG4 and IgE, which have been studied extensively in adult populations, are influenced by gender and by the degree of filarial endemicity during childhood. Development of specific IgG4 and IgE was examined in 502 children aged 3 months to 12 years, who were resident in 3 villages in South-Sulawesi with microfilaria prevalences of 6, 23 and 42%. Specific IgG4 and IgE could be detected as early as 18 months after birth, in low amounts, and increased to levels comparable to those produced by adults at the age of 3 years. A higher prevalence of anti-filarial IgG4 in boys, indicating higher filarial infection compared to girls, became apparent after the age of 7. The specific IgG4 response was strongly influenced by the degree of filarial endemicity and production of this antibody was considerably delayed in the low transmission village. With respect to IgE, it was noted that specific IgE was consistently higher in boys from infancy onwards indicating a predisposition for high IgE production in males. The influence of filarial endemicity was less profound on IgE than on IgG4. In conclusion, reactivity to filarial antigens begins early in life and is differentially influenced by gender and transmission intensity.