Mexico has shown an increase in dengue incidence rates. There are factors related to the location that determine housing infestation by Aedes. This study aimed to determine factors associated with housing infestation by immature forms of Aedes spp. in the dengue endemic localities of Axochiapan and Tepalcingo, Mexico, from 2014 to 2016. A cohort study was carried out. Surveys and inspections of front- and backyards were conducted every 6 months, looking for immature forms of Aedes spp. A house condition scoring scale was developed using three variables (house maintenance, tidiness of the front- and backyards, and shading of the front- and backyards). Multiple and multilevel regression logistic analysis were conducted considering the housing infestation as the outcome and the household characteristics observed 6 months before the outcome as factors; this was adjusted by time (seasonal and cyclical variations of the vector). The infestation oscillated between 5.8% of the houses in the second semester of 2015 and 29.3% in the second semester of 2016. The factors directly associated with housing infestation by Aedes were the house condition score (adjusted odds ratio [aOR]: 1.64; 95% CI: 1.40-1.91) and the previous record of housing infestation (aOR: 2.99; 95% CI: 2.00-4.48). Moreover, the breeding-site elimination done by house residents reduced the housing infestation odds by 81% (95% CI: 25-95%). These factors were independent of the seasonal and cyclical variations of the vector. In conclusion, our findings could help to focalize antivectorial interventions in dengue-endemic regions with similar demographic and socioeconomic characteristics.