Use of nature-derived matrices of a part of body tissues has been used to repair damaged tissues in practical terms. Recently, the same idea has also been applied to regenerate whole organs including the heart, liver, lung, and pancreas etc. Thus, so-called bio-artificial organ technology becomes a promising way of overcoming the lack of donor organs and immune rejections in organ transplantation if we can obtain recipient stem cells. Although the regenerated heart in vitro so far may demonstrate some typical organ's responses in vitro and vivo, it is still far from a fully functional organ for transplantation. We initiated a study to look at changes occurring during the generation of bio-artificial organ using the mouse model. Adult hearts were dissected out and perfused for acellularization with SDS-containing buffer and washed several times. Enzymatic treatment also evaluated the acellular purity by isolating genomic DNA and total RNA before and after DNase and RNase treatments. For recellularization, differentiating H9C2 cell or cells derived from P19 EC cells along with mesenchymal stem cells were seeded on the finally obtained heart matrix several times before submerging culture for generating the heart. Histological analyses revealed that complete removal of cellular components. The intensive staining of alcian blue (pH 1.5 and 2.5) suggests that acid mucopolysaccharides, glycocomponents and sulfate-containing saccharides are widely spread within the heart matrix. There was little DNA and RNA in the heart matrix after the enzymatic treatments as judging by the DAPI or PI staining. Cell seeding and subsequent submerging culture showed substantial heart tissue development as evidenced by immunocytochemistry and RT-PCR in the recellularized and grown heart. From these results, we suggest that each procedure for bio-artificial organ has to be carefully examined to improve the entire process.