Background: Pyrethroid and organophosphate resistance in the malaria vector Anopheles gambiae has led to the search for not only alternative insecticides, but also repellent chemical compounds. However, little is known about the potential actions of repellents and the cross-resistance risk between insecticide and repellent compounds. Methods: Here we show the action of permethrin, DEET, geraniol, carvacrol, culminaldehyde and cinnamaldehyde against three A. gambiae strains: 'Kis' (Kisumu susceptible strain), 'KdrKis' (pyrethroid resistant strain) and 'AcerKis' (organophosphate resistant strain), the last two differing from the first by a mutation on the kdr and ace1 genes, respectively. Conclusions: Results from the DEET assays show it induced repellency for the resistant KdrKis and AcerKis strains but maintained irritancy for the susceptible strain. More generally, we show resistance genes modify the behavior of An. gambiae, increasing or decreasing the effectiveness of DEET and natural compounds, depending on the mutation. These findings offer a new avenue for research on the target and mechanism of repellent compounds. We discuss these findings in the context of vector control strategies.