A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to find metabolic pathways: constraint-based modelling and graph-theoretical path finding approaches. In constraint-based modelling, one aims to find pathways where metabolites are balanced in a pseudo steady-state. Constraint-based methods, such as elementary flux mode analysis, have typically a high computational cost stemming from a large number of steady-state pathways in a typical metabolic network. On the other hand, graph-theoretical approaches avoid the computational complexity of constraint-based methods by solving a simpler problem of finding shortest paths. However, while scaling well with network size, graph-theoretic methods generally tend to return more false positive pathways than constraint-based methods. In this paper, we introduce a computational method, ReTrace, for finding biochemically relevant, branching metabolic pathways in an atom-level representation of metabolic networks. The method finds compact pathways which transfer a high fraction of atoms from source to target metabolites by considering combinations of linear shortest paths. In contrast to current steady-state pathway analysis methods, our method scales up well and is able to operate on genome-scale models. Further, we show that the pathways produced are biochemically meaningful by an example involving the biosynthesis of inosine 5'-monophosphate (IMP). In particular, the method is able to avoid typical problems associated with graph-theoretic approaches such as the need to define side metabolites or pathways not carrying any net carbon flux appearing in results. Finally, we discuss an application involving reconstruction of amino acid pathways of a recently sequenced organism demonstrating how measurement data can be easily incorporated into ReTrace analysis. ReTrace is licensed under GPL and is freely available for academic use at http://www.cs.helsinki.fi/group/sysfys/software/retrace/ ReTrace is a useful method in metabolic path finding tasks, combining some of the best aspects in constraint-based and graph-theoretic methods. It finds use in a multitude of tasks ranging from metabolic engineering to metabolic reconstruction of recently sequenced organisms.