ABSTRACT BACKGROUND: The authors of randomized controlled trials will usually claim that they have met the randomization process criterion. However, sequence generation schemes differ and some schemes that are claimed to be randomized are not genuinely randomized. Even less well understood, and often more difficult to ascertain, is whether the allocation was really concealed. OBJECTIVE: To detect the extent of control over selection bias, in a comparison between two Cochrane groups: oral health and otorhinolaryngology; and to describe the methods used to control for this bias. DESIGN AND SETTING: Cross-sectional study conducted in a public university in São Paulo, Brazil. METHODS: The risk of selection bias in 1,714 records indexed in Medline database up to 2018 was assessed, independent of language and access. Two dimensions implicated in the allocation were considered: generation of the allocation sequence; and allocation concealment. RESULTS: We included 420 randomized controlled trials and all of them were evaluated to detect selection bias. In the sample studied, only 28 properly controlled the selection bias. Lack of control over selection bias was present in 80% of the studies evaluated in both groups. CONCLUSION: The two groups were similar regarding control over selection bias. They are also similar to the methods used. The dimension of allocation concealment appears to be a limiting factor with regard to production of randomized controlled trials with low risk of selection bias. The quality of reporting in studies on oral health and otorhinolaryngology is suboptimal and needs to be improved, in line with other fields of healthcare.