Objective To estimate the prevalence of microcephaly and central nervous system (CNS) defects during the Zika virus (ZIKV) epidemic in Colombia and proportion attributable to congenital ZIKV infection. Study design Clinical and laboratory data for cases of microcephaly and/or CNS defects reported to national surveillance between 2015 and 2017 were reviewed and classified by a panel of clinical subject matter experts. Maternal and fetal/infant biologic specimens were tested for congenital infection and chromosomal abnormalities. Infants/fetuses with microcephaly and/or CNS defects (cases) were classified into broad etiologic categories (teratogenic, genetic, multifactorial, and unknown). Cases classified as potentially attributable to congenital ZIKV infection were stratified by strength of evidence for ZIKV etiology (strong, moderate, or limited) using a novel strategy considering birth defects unique or specific to ZIKV or other infections and laboratory evidence. Results Among 858 reported cases with sufficient information supporting a diagnosis of microcephaly or CNS defects, 503 were classified as potentially attributable to congenital ZIKV infection. Of these, the strength of evidence was considered strong in 124 (24.7%) cases; moderate in 232 (46.1%) cases; and limited in 147 (29.2%). Of the remaining, 355 (41.4%) were attributed to etiologies other than ZIKV infection (syphilis, toxoplasmosis, rubella, cytomegalovirus, herpes 1 and herpes 2 viruses only, n = 32 [3.7%]; genetic, n = 16 [1.9%]; multifactorial, n = 42 [4.9%]; unknown, n = 265 [30.9%]). Conclusions Fifty-eight percent of cases of microcephaly and/or CNS defects were potentially attributable to congenital ZIKV infection; however, the strength of evidence varied considerably. This surveillance protocol might serve as a model approach for investigation and etiologic classification of complex congenital conditions. (J Pediatr 2020;222:112-9). See editorial, p 15 I n 2015, the Colombian National Institute of Health (INS) began Zika virus (ZIKV) surveillance, including protocols for testing and management of pregnant women and infants with suspected ZIKV infection. 1,2 In 2016, the World Health Organization declared a Public Health Emergency of International Concern prioritizing global efforts to prevent ZIKV transmission and to perform surveillance for ZIKV transmission and for adverse outcomes related to congenital ZIKV infection, including microcephaly and birth defects of the central nervous system (CNS). 3-6 Building on its existing birth defects surveillance infrastructure, the INS established an enhanced surveillance protocol focused on microcephaly and CNS defects to monitor potential increases in birth prevalence; identify possible causes, including congenital ZIKV infection; determine proportion of reported cases potentially attributable to ZIKV; and direct appropriate public health intervention. The first confirmed case of ZIKV-related congenital microcephaly in Colombia was reported in April 2016. 7 A preliminary report of surveillance