The prevalence of allergic diseases, such as bronchial asthma, atopic dermatitis, nasal allergies (pollinosis), and food allergies, has been increasing in many countries. The hygiene hypothesis was recently considered from the perspective of exposure to antimicrobial agents and preservatives, such as parabens (CAS number, 94-13-3). It currently remains unclear whether parabens, which are included in many daily consumer products such as cosmetics, shampoos, and personal care products as preservative antimicrobial agents, induce or aggravate allergies. Therefore, the aim of the present study was to examine the relationship between exposure to parabens and the prevalence of allergic diseases in Japanese children. The cross-sectional epidemiology of 236 children aged 0–3 years who underwent health examinations in Shika town in Japan assessed individual exposure to parabens using urinary concentrations of parabens. The results obtained showed that the prevalence of atopic dermatitis was significantly higher in children with high urinary concentrations of parabens than in those with low concentrations (p < 0.001). This relationship remained significant after adjustments for confounding factors, such as age, sex, Kaup’s index, and passive smoking (p < 0.001). In conclusion, the present results from a population study suggested a relationship between atopic dermatitis and exposure to parabens. A longitudinal study using a larger sample number and a detailed examination of atopic dermatitis, including EASI scores and exposure to parabens, will be necessary.