BACKGROUND: A method has been developed to estimate a fitness landscape experienced by HIV-1 under treatment selective pressure as a function of the genotypic sequence thereby also estimating the genetic barrier to resistance. METHODS: We evaluated the performance of two estimated fitness landscapes (nelfinavir [NFV] and zidovudine [AZT] plus lamivudine [3TC]) to predict week 12 viral load (VL) change for 176 treatment change episodes (TCEs) and probability of week 48 virological failure for 90 TCEs, in treatment experienced patients starting these drugs in combination. RESULTS: A higher genetic barrier for AZT plus 3TC, (quantified per additional mutation required to develop resistance against these drugs) was associated with a 0.54 (95% confidence interval [CI] 0.30-0.77) larger log10 VL reduction at 12 weeks (P < 0.0001) and a 0.39 (95%/ CI 0.23-0.66) lower odds of virological failure at 48 weeks (P = 0.0005), in analyses adjusting for the pre-TCE VL and the exact time-lag between the TCE and the date of determining response VL. The strength of these associations was comparable with those seen with expert interpretation systems (Rega, ANRS and HIVDB). A higher genetic barrier to NFV resistance was the only genotypic predictor that tended to be associated with a 0.19 (95% CI 0-0.39) higher log10 VL reduction at 12 weeks (P = 0.05) and a 0.63 (95% CI 0.36-1.09) lower odds of virological failure at 48 weeks ( P = 0.10) per additional mutation. CONCLUSIONS: These results suggest that an estimated genetic barrier derived from fitness landscapes may contribute to an improvement of predicted treatment outcome for NFV and this approach should be explored for other drugs.