Background Over the past 30 years the prevalence of atopic diseases has been increasing worldwide, especially in developed Western countries. It is not known if the prevalence of atopic diseases in the Netherlands has continued to rise, decreased, or plateaued since 2014. We aimed to determine the incidence and prevalence of childhood atopic dermatitis, asthma, allergic rhinoconjunctivitis, and the atopic triad in primary care. Methods A retrospective cohort study within the Rijnmond Primary Care Database consisting of electronic primary care health records. Results Between 2013-2021 22,123 children were available for analysis. The prevalence rate for atopic dermatitis was 8.4 per 100 patient years (PYs); for asthma 4.2 per 100 PYs; and for allergic rhinoconjunctivitis 5.3 per 100 PYs. The average prevalence of the atopic triad was 0.22 per 100 PYs. Median age of disease-onset and peak prevalence for atopic dermatitis was at three years for both outcomes; for asthma at nine and seventeen years; and for allergic rhinoconjunctivitis at 10 and 17 years, respectively. Conclusions Atopic diseases are prevalent among the childhood primary care population of Rijnmond and we observed increasing incidence and prevalence rates for allergic rhinoconjunctivitis. Atopic dermatitis had its peak prevalence at the youngest age, and is followed by asthma and allergic rhinoconjunctivitis. Further, we found a significant sex disparity for all atopic diseases.