A frequency-domain realization theory is developed for the class of autonomous- , but not necessarily stationary, boundary-value linear systems. It is shown that this realization problem, which consists of constructing autonomous boundary-value linear systems from prescribed weighting patterns, reduces to the factorization of several rational matrices in two variables having separable denominators. This factorization problem is examined and a method is given for constructing minimal factorizations for such rational matrices. The special case of stationary systems is also considered.