We investigated the prevalence of congenital renal and urologic anomalies in children with congenital hypothyroidism to determine whether further renal and urologic investigations would be of benefit. Prevalence of congenital hypothyroidism was obtained from the New York State Congenital Malformation Registry. The occurrence of urinary tract anomalies were calculated for children with congenital hypothyroidism and compared to children without congenital hypothyroidism. In addition we obtained congenital hypothyroidism data from New York State newborn screening, and the cases were matched to Congenital Malformation Registry. Analysis of Congenital Malformation Registry data showed 980 children with congenital hypothyroidism and 3 661 585 children without congenital hypothyroidism born in New York State (1992-2005). Children with congenital hypothyroidism have a significantly increased risk of congenital renal and urological anomalies with the odds ratio (OR) of 13.2 (10.6-16.5). The other significantly increased defects in congenital hypothyroidism were cardiac, gastrointestinal, and skeletal. Analysis of matched data confirmed an increase of congenital renal and urologic anomalies with OR of 4.8 (3.7-6.3). Children with congenital hypothyroidism have an increased prevalence of congenital renal and urologic anomalies. We suggest that these children should be evaluated for the presence of congenital renal and urologic anomalies with renal ultrasonography, and that further studies of common genes involved in thyroid and kidney development are warranted.