In order to determine the frequency and variety of cis-regulatory elements that function during embryonic development of Strongylocentrotus purpuratus, we constructed a GFP expression vector in which to test the activity of randomly chosen genomic DNA fragments that includes a promiscuous basal promoter from the endo16 gene. This vector was demonstrated to serve as a cis-regulatory element trap. We used it to carry out an initial test for the occurrence of elements that would promote GFP expression in this genome. In the screen reported here 108 different randomly chosen DNA fragments (av. 3.8 kb) were inserted in the vector, and each was injected into > 200 zygotes. Surprisingly, 13% of the fragments tested yielded detectable levels of GFP expression in the recipient embryos. Specific patterns observed included expression in endoderm, in aboral ectoderm, and in pigment cells. The majority of active constructs expressed GFP in all spatial domains of the embryo. Elements with detectable cis-regulatory activity in the embryo occur in the sample screened, on the average, about every 30 kb, and the genome must include many thousands of such elements. On further analysis one isolate was shown to contain a gut specific element as well as one that controls expression in the secondary mesenchyme cells.