Insecticides are still largely applied in public health to control disease vectors. In Brazil, organophosphates (OP) and pyrethroids (PY) are used against Aedes aegypti for years. Since 2009 Insect Growth Regulators (IGR) are also employed in the control of larvae. We quantified resistance to temephos (OP), deltamethrin (PY), and diflubenzuron (IGR) of A. aegypti samples from 12 municipalities distributed throughout the country, collected between 2010 and 2012. High levels of resistance to neurotoxic insecticides were detected in almost all populations: RR95 to temephos varied between 4.0 and 27.1; the lowest RR95 to deltamethrin was 13.1, and values higher than 70.0 were found. In contrast, all samples were susceptible to diflubenzuron (RR95 < 2.3). Biochemical tests performed with larvae and adults discarded the participation of acetylcholinesterase, the OP target, and confirmed involvement of the detoxifying enzymes esterases, mixed function oxidases, and glutathione-S-transferases. The results obtained were discussed taking into account the public chemical control component and the increase in the domestic use of insecticides during dengue epidemic seasons in the evaluated municipalities.