Tomato genome sequencing projects have started to become an internationally coordinated program. To accelerate tomato functional genomics studies in coordination with the complete sequencing of the tomato genome, we prepared a full-length cDNA library from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom, which has attracted attention as a laboratory-grown model plant. Total RNA from maturing fruits was subjected to a vector-capping protocol for full-length cDNA synthesis. We generated 8,046 expressed sequence tags (ESTs), which comprised 3,484 contigs. We calculated that 80.7% of the cDNA clones in the library met the criteria for full-length clones, and 1,920 non-redundant full-length clones were identified. As a pilot experiment, we chose seven clones, whose encoded proteins shared low homology with Arabidopsis proteins, for full sequencing. Of these, three genes had no or very low homology with Arabidopsis genes, indicating the usefulness of the library for analyses of “not-found-in-Arabidopsis” genes.