Objective: To describe a case of congenital syphilis with a late diagnosis and identify missed opportunities at diverse phases/levels of healthcare, which led to late diagnosis. Case description: Boy, 34 days of life, referred from a basic healthcare unit to a tertiary hospital due to enlarged abdominal volume and progressive jaundice for 2 weeks, fecal hypocholia, hepatosplenomegaly, anemia, low platelet count and elevated liver enzymes. At physical examination, the infant presented with erythematous-exfoliative lesions on the palms and soles, macular rash in the inguinal region, ascitis, palpable liver 5 cm below the right costal margin and a palpable spleen 3 cm from the left costal margin. Infant serology: reactive CMIA (chemiluminescent microparticle immunoassay), VDRL (Venereal Diseases Research Laboratory) 1:1024 and reactive TPHA (Treponema pallidum Hemagglutination). Maternal serology: reactive CMIA and TPHA, VDRL 1:256. Radiography of the long bones showed symmetric periostitis, periosteal thickening, and lucent bands in the femur, humerus, ulna and tibia. After treatment with crystalline penicillin, the infant showed clinical and laboratory improvement, receiving hospital discharge at the 18th hospitalization day. Comments: This case shows that congenital syphilis is occasionally diagnosed late as a result of failed strategies to prevent this disease, both in the basic and secondary/tertiary levels of care. The application of interventions recommended by the Ministry of Health and identification of the situation in which there is ineffective implementation of these measures are important to assess routine care in all levels of healthcare and diverse units responsible for newborn and infant health care. [ABSTRACT FROM AUTHOR]