Background There is a paucity of population-based surveys on oral health conditions in Ecuador. Thus, the aim of this study was to conduct an epidemiological survey with a representative sample of children aged 12 years from public schools of Quito, Ecuador. The aim of this initial report was to describe the methodology used in the survey, as well to present results regarding calibration procedures and prevalence of oral-health related outcomes. Methods We invited 33 public schools’ coordinators from the urban area of Quito, and 1100 children (12 years old) to take part in this study. Six trained and calibrated examiners conducted clinical examinations using oral mirrors and ball-ended probes to assess: dental caries, traumatic dental injuries, malocclusion, gingival bleeding, presence of calculus and fluorosis. Children also responded a questionnaire on Oral Health-Related Quality of Life (OHRQoL). Individual sociodemographic data was collected through a questionnaire sent to parents. Moreover, some contextual data on school environment (infrastructure conditions, promotion of health practices and negative episodes) were also evaluated. Prevalence values, crude and weighted by sampling weights, and 95% confidence intervals (95%CI) were calculated. Results Nine hundred and ninety-eight children from 31 schools were examined from March to May 2017. The adjusted prevalence values (95%CI) for the six outcomes evaluated were: dental caries = 60.3% (55.3 to 65.0%); traumatic dental injuries = 20.7% (17.2 to 24.8%); dental fluorosis = 63.7% (58.5 to 68.5%); gingival bleeding = 92.0% (87.1 to 95.2%); presence of calculus = 69.9 (60.5 to 77.9%); and malocclusion = 25.8% (21.8 to 30.3%). Adjusted mean of number of decayed, missed or filled permanent teeth (DMF-T) was 1.61 (1.37 to 1.84). Results on OHRQoL and other contextual variables will be reported in other articles. Conclusion The prevalence of the majority of oral health problems in 12-year-old children from public schools in Quito-Ecuador was compatible with those observed in other similar cities. However, periodontal health and fluorosis seem to be highly prevalent in children from Quito. Electronic supplementary material The online version of this article (10.1186/s12903-019-0863-9) contains supplementary material, which is available to authorized users.