Differential gene expression analysis has been investigated to reveal important genes in many plant species. Identification of genes controlling metabolic pathways in garlic could contribute to the understanding of garlic genetic. In this study, transcript (mRNA) profile of differentially expressed genes was determined in leaf, meristematic and flower tissues of three genetically divers garlic clones at different developmental stages using cDNA-AFLP approach. In total, 352 differentially expressed transcript-derived fragments (TDFs) were evaluated from 20 primer combinations. While seven TDFs fragments expressed only in meristematic tissues, 30 TDFs expressed only in leaf tissues. Twenty seven fragments expressed in both meristematic and leaf tissues with intensity polymorphism and two fragments differentially expressed in flower tissues. BLAST analysis of these tissue specific expressed fragments revealed that some genes have significant similarities with previously determined sequences in the database of NCBI GenBank while some of them are unique to garlic genome. These tissue specific expressed genes can be used to develop tissue specific markers for garlic genome.