Objectives. To determine the ratio of microcephaly in newborns in level II and III health facilities of the Ministry of Health (MINSA) of Peru for the period 2005-2013. Materials and Methods. A secondary analysis of the databases of the Perinatal Information System was carried out during 2005-2013. Microcephaly was identified applying World Health Organization (WHO), Fenton, mixed (WHO-Fenton), and proportionality criteria. The ratios and indices of microcephaly were estimated per 10,000 live births (LB) by region and concordance was compared, using the WHO parameter as a reference. Results. The ratio of microcephaly during 2005 to 2013 was 3.4%, the average rate of microcephaly was 335 per 10,000 LBs according to the WHO criterion. The mixed parameter showed a substantial concordance (Kappa of 0.635), while the proportionality parameter showed a reasonable concordance (Kappa of 0.298). Conclusions. The ratio of microcephaly in MINSA Level II and III health facilities was higher than that reported in other countries in the region before the appearance of Zika in the Americas. The frequency variations observed with those of other countries and among Peruvian regions could be explained by different factors, such as the technique for measuring head circumference, data capture, constitutional factors, and social determinants. We suggest standardizing measurements and their recording, harmonizing diagnostic criteria, and establishing health strategies to strengthen the epidemiological surveillance of the causes of microcephaly.