PURPOSE: To compare the production of the phoneme /r/ in children with phonological disorder (PD) and the stomatognathic system (SS) alterations considering the variables age, gender, and severity of the PD. METHODS: The sample was composed by 113 subjects with PD and SS alterations, of both genders, and with ages between 4 years and 8 years and 11 months, divided into two groups, considering the age range: pre-school age (4 years to 5 years and 11 months), and school age (6 years to 8 years and 11 months). The Child's Phonological Assessment and a stomatognathic system evaluation were carried out. The subjects were divided into two groups, according to the severity of PD: More Severe Degrees (MSD) and Milder Degrees (MD). Considering the phonological system, subjects were divided into GI: /r/ established, and GII: /r/ not established. The collected data were tabulated, analyzed and submitted to statistical analysis. RESULTS: No differences were observed between GI and GII regarding tongue, lips and cheeks position, tonicity and mobility, as well as in SS structures and functions. GI obtained better performance only in tongue vibration. It was verified a correlation between the acquisition of phoneme /r/ and age increase; no correlation was found between the acquisition of /r/ and gender. MSD of PD were more frequent in GII, and MD in GI. CONCLUSION: There is no relation between alterations in the PS and in structures and functions of the SS in children with PD; PD is related only with children's age.