to describe the prevalence coefficients and characterize cases of microcephaly at birth in Brazil from 2000-2015.this is a descriptive study with data from the Information System on Live Births (Sinasc). The coefficients were calculated by region and characteristics of mothers and live births (LB).the annual average number of microcephaly cases was 164 for the period 2000-2014, whilst in 2015, 1,608 cases were registered (54.6 cases per 100 thousand LB). Higher coefficients were observed among preterm babies (81.7; 95%CI 72.3;92.2), born from black-skinned (70.9; 95%CI 58.5;85.9) or to brown-skinned (71.5; 95%CI67.4;75.8) women, to women aged ≤19 (70.3; 95%CI 63.5;77.8) or ≥40 (62.1; 95%CI 46.6;82.6), with ≤3 years of study (73.4; 95%CI 58.2;92.4) and residents in the Northeast region (138.7; 95%CI 130.9;147.0).the high number of microcephaly cases in 2015 reinforces the importance of Sinasc and the need to improve the surveillance of congenital anomalies.