Preoperative and postoperative serum samples of 35 patients with different congenital gastrointestinal anomalies were analyzed for the markers CEA, CA 125 and 19-9 by immunoradiometric assay during a period of three years. The majority of the anomalies were aganglionic megacolon and hypertrophic pyloric stenosis. CA 125 and CA 19-9 were likely to indicate logistic model probabilities for babies with anomalies, while CEA was not (F=35.78, p<0.05 for CA CA 125 and F=4.36, p<0.05 for CA 19-9). Probability of no congenital anomaly for babies was: p (Normal)=e4.41-0.13CA125 - 0.05CA19-9/1+e4.41-0.13CA125- 0.05CA19-9 Using CA 125 as a marker, babies with congenital anomalies were determined with 83.3 percent probability (F= 11.33, p<0.05). On the other hand, it was not possible to predict the type of anomaly with these three markers. CEA, CA 125 and CA 19-9 seem to be prognostic variables associated with congenital anomalies. These biological markers provide information that can be incorporated into the diagnosis of anomalies but without doubt results of markers should be supported by clinical findings.