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Sexually transmitted infections (STIs) represent a worldwide public health burden, but many infections and diseases continue to be neglected. Areas with a low human development index, including the northern areas of Brazil, particularly the immense geographic Amazon region, present a high frequency of STIs because of variables that contribute to disseminate the infection, including lack of access to education, prevention measures and treatment to these vulnerable population groups. This review describes the chronological investigation of the etiology of pathologies associated with infection by <i>Chlamydia trachomatis</i>, including its prevalence, distribution, and clinical, descriptive and molecular epidemiology in regard to STIs, trachoma and heart disease. Long-term investigations among urban and nonurban populations are discussed and show the need for and effects of continuous surveillance to diminish the burden among vulnerable populations (female sex workers, quilombos and indigenous peoples) and to define new etiological associations of diseases with infections by <i>C. trachomatis</i>.