A laboratory testing algorithm was evaluated to confirm West Nile virus (WNV) infection in human serum following the introduction of the virus in Puerto Rico in 2007. This testing algorithm used two standard diagnostic assays, the IgM antibody capture enzyme-linked immunosorbent assay (MAC ELISA) and real-time reverse transcriptase PCR (RT-PCR), along with two nonconventional assays, the nonstructural protein 1 (NS1) ELISA and a 90%-plaque-reduction neutralization test (PRNT(90)) with IgG depletion for dengue virus (DENV) and WNV. A total of 2,321 serum samples from suspected WNV human cases were submitted for testing. Approximately one-third (867, 37%) were cross-reactive for DENV and WNV by MAC ELISA and had negative RT-PCR results for both viruses. Of a subset of 43 samples tested, 31 (72%) of these cases were identified as positive for DENV in the PRNT(90) with IgG depletion and 8 (19%) were positive in the DENV NS1 antigen ELISA. These two assays combined differentiated 36 (84%) of the samples that could not be diagnosed using the standard diagnostic testing methods.