We have introduced a new methodological approach called SeqTrack for the analysis of genetic data sampled during disease outbreaks. Using simulated data, we showed the originality of this method compared to classical phylogenetic reconstruction, and its ability to infer correct genealogies of isolates in densely sampled disease outbreaks. The reconstruction of transmission trees from genetic data has recently received considerable attention (Gonzalez-Candelas et al., 2003; Hue et al., 2005; Cottam et al., 2008a; Cottam et al., 2008b; Harris et al., 2010) . All previous applications we are aware of have been based on the reconstruction of most recent common ancestors. Although this body of work has been fairly successful, the simulations presented in this paper suggest that our method outperforms phylogenetic approaches for the reconstruction of transmission trees in intensively sampled disease outbreaks. Even when taking temporal information into account, phylogenetic reconstruction seems unable to infer filiations between sampled isolates. This statement does not amount to a criticism of phylogenetics but simply reflects the fact that transmission trees and phylogenies are actually different entities. As such, transmission trees are likely to be inferred more successfully by a dedicated approach. Our method is also not meant to supersede phylogenetic approaches but rather to complement them. Although SeqTrack is better suited for reconstructing the transmission tree during early outbreaks, it does not include some useful features of modern phylogenetic tools, such as the possibility to infer underlying population dynamics parameters.