A dramatic increase in twin pregnancies has been observed in the past few decades, primarily related to assisted reproductive techniques (ART) and increased average maternal age during pregnancy. Multiple pregnancies, compared to singleton pregnancies, are associated with greater perinatal morbidity and mortality. The present study evaluated the perinatal outcomes of pregnancies with discordant anomalous twins in a tertiary maternity ward in a developing country. Data were retrospectively collected from the Instituto Fernandes Figueira/FIOCRUZ, Brazil between January 2002 and December 2014. We identified 74 twin pregnancies with discordant anomalous twins. Final data analysis was based on 40 pregnancies. Congenital defects were classified according to the International Classification of Diseases: ICD-10: the digestive system was responsible in 27 (34%) cases; the central nervous system was responsible in 18 (22%) cases; the urinary tract was responsible in 14 (17%) cases; and the circulatory system was responsible in 14 (17%) cases. A total of 19 deaths occurred during the study period, and delivery before 30.4 weeks was a significant prediction of fetal death (p = .01). The presence of hydrops in the affected fetus was related to a higher number of deaths in healthy fetuses and contributed to a worse prognosis. The presence of this condition was the cause of 12 (55.6%) deaths in healthy fetuses. A 10 times higher risk of death of a normal co-twin was observed in cases of death of the anomalous twin (p = .002, OR 10.55, 95% CI: 1.9–58.52).