Introduction: Children with chronic non-progressive encephalopathy (NPE) may present gastro-esophageal reflux disease (GERD) associated to neurogenic oropharingeal dysphagia. As clinical symptoms of children with NPE are in part similar to those with GERD, diagnostic doubts may arise. We therefore aimed to verify clinical and swallowing aspects in these children and the frequency of GERD in NPE. Methods: We studied 73 children paired for age (1mo-6y) and gender, in groups: 25 control (C); 23 suspicious of GERD (R), without encephalopathy and any dysphagia for at least 2mo (previous crises of cough, choking and/or cyanosis in 19); 25 NPE with clinical oropharingeal dysphagia (E). Semi-structured questionnaires about symptoms and oral habits were applied, bottle, pacifier and digital sucking above 2 years of age being considered deleterious. Morpho-functional aspects of orofacial structures and swallowing without food were evaluated. At least 1 positive test diagnosed GERD. Non-parametric statistics were used. Results: Median age was 25mo, 60.3% male. Birth was more frequently premature in R (82.6%) than in C (28%) and intermediate for E (p<.001). Weight/age and height/age were lower in R and E than in C (p<.001), but weight/height was lower only for E, intermediate for R (p<.005). The frequencies of most digestive and respiratory manifestations were similar in R and E, as well as irritability, nasal regurgitation, hoarseness after feeding, mothers attempts to improve deglutition (change in food consistency and temperature), all absent in C. R and E less frequently ingested food pieces than C (p<.05). Only vomiting and change in body position at/after ingestion were more frequent in R than in E, and cough/choking and/or cyanosis at ingestion more frequent in E than in R. Orofacial structures were altered more frequently in E (p<.001), but often present also in R and C, perhaps due to similar deleterious oral habits. Swallowing was altered in 80% of E, but in only 1 child of R (4,3%). GERD was diagnosed in 68% of E children. Conclusion: It was concluded that E was nutritionally more affected than R. Most clinical symptoms were similar for R and E but disordered deglutition and alterations in orofacial structures predominated in E. GERD was frequent in E, therefore, neurogenic dysphagia as well as GERD contribute to symptoms. Nasal regurgitation and hoarseness after feeding in R, point to oropharingeal dysphagia, possibly secondary.