Objective The aim of this work was to investigate in more detail the dental clinical features that could serve to define subphenotypes of oral clefts. Design Dental records of oral cleft subjects from a group of 164 cases were examined, and 157 were included in this study. In addition, 65 families with two or more siblings born with clefts and 30 control families were evaluated to determine whether dental phenotypes were sporadic. Type of oral cleft and dental phenotypes (tooth agenesis, supernumerary teeth, taurodontism, dental transposition, and microdontia) outside the cleft area were investigated. Association of dental anomalies with preferential subtypes of cleft (subphenotype) was assessed. Results A total of 74 subjects presented at least one developmental dental anomaly. Tooth agenesis was the most common dental anomaly (28.6%), followed by taurodontism (15.2%). Supernumerary teeth were associated with cleft palate only ( p = .05). The absence of maxillary left lateral incisors was significantly associated with unilateral right cleft lip ( p = .02). Bilateral clefts were strongly associated with bilateral dental anomalies ( p < 0.001). In the cleft lip and palate group, tooth agenesis was associated with dental transposition ( p = .03) and with supernumerary teeth ( p = .009). Subjects with oral clefts have a higher risk of tooth agenesis (odds ratio = 3.33; 95% confidence interval, 1.18 to 10.13) and taurodontism (odds ratio = 3.95; 95% confidence interval, 2.28 to 6.82). Tooth agenesis, microdontic upper lateral incisors, and supernumerary teeth were most commonly found in unaffected siblings and parents of children born with clefts in comparison with families with no family history of clefts ( p = .01). Conclusion The preferential associations between specific cleft types with dental phenotypes suggest dental anomalies can be used as clinical markers to define the subphenotype isolated cleft lip and palate.