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Medicago truncatula serves as a model plant for legume genetics and genomics. We used RNA-Seq to characterize the transcriptome during the early organogenesis of the nodule and during its functioning. We generated approximately 135.5 million high-quality 36-bp reads, which were then aligned with the M. truncatula genome sequence (Mt3.0 version) and with sequences from a custom splice-junction database, for the detection of transcribed regions and splicing sites. Mapping and analysis of the reads conducted to the detection of 37,333 expressed transcription units (TUs), 1,670 had never been described before and were functionally annotated. We identified 7,595 new transcribed regions, mostly corresponding to 5’ and 3’ UTR extensions and new exons associated with 5,264 previously annotated genes. We also assessed the complexity in the nodulation transcriptome by performing a Cufflinks analysis to determine the frequency of the various alternatively spliced forms. Thus, we identified 23,164 different transcripts derived from 6,587 genes. Finally, we carried out a differential expression analysis, which provided a comprehensive view of transcriptional reprogramming during nodulation.All Illumina sequence data have been deposited in the NCBI short-read archive, and Sanger-sequenced PCR products have been deposited in GenBank (SRA048731). Assembled contigs longer than 200 bp have been deposited at TSA (JR366937-JR375780). Coverage data are available at http://ddlab.sci.univr.it/cgi-bin/gbrowse/medicago/.