If only about 4 of every 100 patients beginning their first anti-HIV drugs were infected with resistant virus, primary genotypic resistance testing would cost $69,000 per QALY gained. If 20 of every 100 had resistant virus, then primary resistance testing would cost $22,300 per QALY gained. Secondary resistance testing was estimated to cost about $17,000 per QALY gained. On the basis of these findings, and compared with many other accepted therapies, genotypic resistance testing can be considered cost-effective.