As with all other anti-HIV drugs, strains of HIV that are resistant to d4T (stavudine, Zerit) may emerge after a period of treatment. The emergence of drug-resistant strains coincides with a fall in the effectiveness of the drug.

There is considerable cross-resistance amongst the nucleoside reverse transcriptase inhibitors (NRTIs). This means that once resistance to one NRTI has developed, other NRTIs will have less effect on HIV viral load.

The response to d4T can be reduced by thymidine analogue mutations (TAMs), including T215Y/F and M41L. Conversely, treatment with d4T may also cause the development of TAMs, which confer resistance to AZT (zidovudine, Retrovir) and abacavir (Ziagen). Since the launch of d4T, there has been considerable debate about whether it is best to start with an AZT- or d4T-based regimen. In the mid-to-late 1990s, d4T was promoted as a useful first-line treatment based on evidence that resistance to d4T was slow to develop and rarely led to cross-resistance. However, as d4T may select AZT-associated mutations and multi-NRTI mutations, superiority of d4T as a first-line nucleoside has been called into question, coupled with d4T’s less favourable side-effect profile.

Other mutations that cause resistance to d4T include D67N, V75T and L210W. The resistance mutations Q151M and 69SS cause resistance to all the NRTIs and may emerge during treatment with d4T.