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Background Understanding the breeding patterns of Aedes aegypti in households and the factors associated with infestation are important for implementing vector control. The baseline survey of a cluster randomised controlled trial of community mobilisation for dengue prevention in Mexico and Nicaragua collected information about the containers that are the main breeding sites, identified possible actions to reduce breeding, and examined factors associated with household infestation. This paper describes findings from the Mexican arm of the baseline survey. Methods In 2010 field teams conducted household surveys and entomological inspections in 11,995 households from 90 representative communities in the three coastal regions of Guerrero State, Mexico. We characterized Ae. aegypti breeding sites and examined the effect of two preventive measures: temephos application in water containers, and keeping the containers covered. We examined associations with household infestation, using bivariate and multivariate analysis adjusted for clustering effects. Results We conducted entomological inspections in 11,995 households. Among 45,353 water containers examined, 6.5% (2958/45,353) were positive for larvae and/or pupae. Concrete tanks (pilas) and barrels (tambos) together accounted for 74% of pupal productivity. Both covering water containers and inserting temephos were independently associated with a lower risk of presence of larvae or pupae, with the effect of covering (OR 0.22; 95% CIca 0.15–0.27) stronger than that of temephos (OR 0.66; 95% CIca 0.53–0.84). Having more than four water containers was associated with household infestation in both rural areas (OR 1.42; 95% CIca 1.17–1.72) and urban areas (1.81; 1.47–2.25), as was low education of the household head (rural: 1.27; 1.11–1.46, and urban: 1.39; 1.17–1.66). Additional factors in rural areas were: household head without paid work (1.31; 1.08–1.59); being in the Acapulco region (1.91; 1.06–3.44); and using anti-mosquito products (1.27; 1.09–1.47). In urban areas only, presence of temephos was associated with a lower risk of household infestation (0.44; 0.32–0.60). Conclusion Concrete tanks and barrels accounted for the majority of pupal productivity. Covering water containers could be an effective means of Ae. aegypti vector control, with a bigger effect than using temephos. These findings were useful in planning and implementing the Camino Verde trial intervention in Mexico.