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BlockMatch is a software tool capable of aligning and comparing two RNA blocks. An RNA block is a structure-annotated multiple RNA sequence alignment represented in Stockholm format. Examples of blocks can be found in Rfam where a seed alignment is a block, or in GLEAN-UTR DB where a group is a block. On this website, we provide a web server that allows the user to input two blocks A and B, and performs either local alignment or global alignment of the two input blocks. The scoring matrix used is the RIBOSUM85-60 matrix. In what follows, sample block A is group 3 taken from GLEAN-UTR DB, which is the Histone 3' UTR stem-loop group in human homologs, and sample block B is the seed alignment taken from the Rfam family RF00032, which is the Histone 3' UTR stem-loop stored in Rfam. The web server compares the two input blocks and displays an alignment score together with a p-value, indicating the significance of the alignment score. A software package is also available for download. In addition, the web server provides a database search function for finding Rfam seed alignments best matching a user-input query block. This search function is able to find and display Rfam families closely related to the query block.