Objectives: To describe aspects of the microcephaly epidemic in the state of Piauí. Methods: All cases of congenital microcephaly confirmed in the state between 2015 and 2016 were included (n = 100). Investigation forms of the Regional Reference Center for Microcephaly were reviewed. Discarded cases (n = 63) were used as a comparison group. Results: In October, November, and December 2015 incidence rates reached 4.46, 6.33 and 3.86/1000 live births, respectively; 44 cases were reported in the state capital. Among the mothers of confirmed and discarded cases, the frequency of skin rash during pregnancy was 50/97 (51.5%) and 8/51 (15.7%), respectively (p < 0.001); 33 confirmed cases (35.9%) had a head circumference z-score between −2 and −3, 23 (25%) between −3 and −4, and 8 (8.7%) had a z-score of less than −4. Head computer tomography scans revealed calcifications in 78/95 (82.1%) cases. Lissencephaly, hydrocephalus and agenesis of the corpus callosum were also frequently observed. Ophthalmic findings included retinal pigment epithelium rarefaction and atrophy. Absence of otoacoustic emissions was observed in 21/70 cases. One newborn also presented lower limb muscle atrophy. There were no significant differences in vaccination rates for influenza, diphtheria-tetanus-acellular pertussis, and hepatitis B in either group.