Congenital Toxoplasma infection can only be discovered or prevented by the appropriate serological screening and subsequent treatment of the mother and her offspring. In Colombia, there is no obligatory Toxoplasma screening for pregnant women and both the reporting and follow-up of congenital toxoplasmosis cases is limited, thereby is a public health problem that have no been addressed by health authorities. The aim of this study was to investigate the occurrence of congenital toxoplasmosis in a public hospital from Armenia, Colombia. A total of 200 serum samples of cord blood were collected. We applied a western blot assay (ID Blot DPC Diagnostics, US) for Toxoplasma IgG, IgM and IgA antibodies that was validated in a cohort of children with confirmed presence or absence of congenital infection. The sensitivity of western blot assay was 91 per cent and the specificity was 100 per cent. In the cord blood samples, we found one infected child that died at day 4 of life and his infection was confirmed by PCR of the B1 specific Toxoplasma gene on brain biopsy. This results show a high prevalence (0.5 per cent, IC95 per cent 0.2–0.8) of Toxoplasma infection in Colombian newborns. Thus, we recommend additional studies to determine the cost-effectiveness of a newborn screening program for congenital toxoplasmosis in other settings in Colombia.