Decoherence-free subspaces (DFSs) are constructed without the assumption of spatially symmetric system-bath coupling. Instead the underlying assumption is that subgroups of the full Pauli group of errors are responsible for the decoherence. The corresponding decoherence-free states can protect quantum information in the presence of multiple-qubit errors, and are stabilizer codes. It is shown how to perform universal fault tolerant quantum computation on this class of DFSs. This is the first demonstration that it is possible to use only one- and two-body quantum gates to perform full-blown quantum computation on a class of DFSs, with a finite number of measurements.