We isolated cells from their native in vivo microenvironment using the Laser Capture Micro dissection (LCM). Bone and cartilage tissues were studied from mouse embryonic (18dpc) processed by cry sections enabled the cell isolation from anatomical complexity of skeletal tissues using the LCM technique. RNA was purified from the isolated cells and followed with amplification stage to hybridize on gene array for high through (HT) put analysis to profile the tissues gene expression. Bioinformatics profiling of the differential expression performed according to the tissue origin highlighted the common and divergent genes in the regulation of these tissues. Specifically, we identified that genes related to cell replication and cell metabolism were more prominent in bone, while organic acid metabolism was more prominent in cartilage. This study has demonstrated the utility of applying HT microarray analysis using RNA from small number of cells isolated by LCM from skeletal tissues. The bioinformatics provides insight which has not yet been explored for the developing skeletal tissues. The power of LCM application provides a platform to make a broad molecular analysis using transcriptom analysis to reveal the molecular signature of tissues in their nature environment.