We study the following rainbow version of subgraph containment problems in a family of (hyper)graphs, which generalizes the classical subgraph containment problems in a single host graph. For a collection G = {G1, G2, . . . , Gm} of not necessarily distinct graphs on the same vertex setthen a rainbow H consists of exactly one edge from each Gi.Our main results are on rainbow clique-factors in (hyper)graph systems with minimum d-degree conditions. In particular,(1) we obtain a rainbow analogue of an asymptotical version of the Hajnal-Szemerédi theorem, namely, if t | n and δ(Gi) ≥ (1, then G contains a rainbow Kt-factor;(2) we prove that for 1 ≤ d ≤ k − 1, essentially a minimum d-degree condition forcing a perfect matching in a k-graph also forces rainbow perfect matchings in k-graph systems. The degree assumptions in both results are asymptotically best possible (although the minimum d-degree condition forcing a perfect matching in a k-graph is in general unknown). For (1) we also discuss two directed versions and a multipartite version. Finally, to establish these results, we in fact provide a general framework to attack this type of problems, which reduces it to subproblems with finitely many colors.