OBJECTIVE: In this study, we intend to identify the prevalence of clinical variables in children with microcephaly.METHODS: This is a cross-sectional and observational study with data collected from medical records of patients admitted to the microcephaly outpatient clinic of a referral center in Teresina-PI. Demographic (gender and age) and clinical data (presence of epilepsy, dysphagia, irritability, and associated comorbidities) were collected. The frequency of Zika virus as a probable etiology was determined from computed tomography patterns and the exclusion of other etiologies by serological tests.RESULTS: A total of 67 patient records were evaluated, of which 31 were male and 36 were female, with a mean age of 1 year and 10 months. The most prevalent clinical variables were epilepsy, present in 47 children (70.2%), and irritability in 37 (55.2%). Also with a high frequency, 22 had dysphagia (32.8%), and 13 had musculoskeletal comorbidities (19.4%). Only three patients in the sample had cardiac abnormalities (4.5%), and no endocrine comorbidity was found. A total of 38 children in the sample (56.7%) presented ZIKV as a probable etiology and, in these cases, there was a higher frequency of epilepsy and dysphagia compared to other etiologies, although not statistically significant.CONCLUSION: Epilepsy, irritability, dysphagia, and musculoskeletal comorbidities were the most frequent clinical variables in children with microcephaly. There was a high prevalence of congenital ZIKV microcephaly syndrome in this sample.