Rural, isolated areas benefit less from caries prevention programs and access to treatment than urban areas, and, hence, differences in oral health can be expected. This study aims to assess the prevalence of caries and malocclusion in urban and rural areas of Peru and to compare them with patients' oral health perception. A total of 1062 adolescents were examined in five schools of rural (Titicaca) and urban (Lima and Cuzco) areas in Peru. Decay Missing Filled Teeth's Surfaces, the Index of Complexity, Outcome and Need and the Child Oral Health Impact Profile short form-19 (COHIP-SF 19) were used to assess caries, severity of malocclusion and Oral Health Quality of Life, respectively. Significant differences in the prevalence (p = 0.001) and degree of caries (p = 0.001) were found between regions. The prevalence of caries was the highest in Cuzco (97.65%), followed by Titicaca (88.81%) and Lima (76.42%). The severity of malocclusion was the lowest in Titicaca. There was a negative relation between malocclusion, caries and COHIP-SF 19, with no evidence of a difference between the regions. This suggests that the higher the prevalence of caries and the more severe the malocclusion, the poorer the perception of oral health. In our study, rural areas presented a lower severity of malocclusion than urban areas.