We sought to determine whether there is an association between choroid plexus cysts identified in the second-trimester fetus and trisomy 21. Over a 7-year period, fetuses scanned between 14 and 22 weeks were prospectively evaluated for the presence of choroid plexus cysts. Follow-up on fetuses with choroid plexus cysts was obtained by review of the medical records. Over the same time period, the scans and reports of all fetuses with trisomy 21 detected in our laboratory by mid-trimester amniocentesis were reviewed. The prevalence of choroid plexus cysts in fetuses with and without trisomy 21 were compared by means of X2 analysis. A total of 473 fetuses with choroid plexus cysts were identified among 32,053 second-trimester fetuses. Sixteen fetuses were lost to follow-up, three had structural defects and normal karyotypes and 21 had abnormal karyotypes, two of which were trisomy 21. Other abnormal karyotypes included trisomy 18, unbalanced translocation and triploidy, previously reported elsewhere. The remaining 433 fetuses either had normal karyotypes or were normal newborns. The prevalence of choroid plexus cysts (excluding fetuses with trisomy 18) was 1.38% in our general population. During the study period, 143 fetuses with trisomy 21 were karyotyped in our laboratory, and two of these (1.40%) had choroid plexus cysts. Both had other sonographic abnormalities suggesting trisomy 21. The difference in prevalence of fetuses with choroid plexus cysts and trisomy 21 vs. those without trisomy 21 was not statistically significant (X2 = 0.98; relative risk (RR) = 1.02; 95% CI = 0.26, 4.03). We conclude that choroid plexus cysts occur with similar frequency in fetuses with trisomy 21 to that in fetuses from the general population. The finding of choroid plexus cysts should not be used to increase the patient's calculated risk of having a fetus with trisomy 21.