AA6061 Aluminum alloy welded joint using two different filler metals were studied by using X-ray CT-Scan. The filler metals ER 4043 and ER 5356 were used in this present work in order to investigate the effect of using different filler metals on the welded joint quality of AA 6061 aluminum alloy in welded zone microstructure. Gas metal arc welding (GMAW) technique and V grove butt joint with four layers and five passes welded joint were performed. From this investigation, it is found that AA6061 with ER 4043 showed less distribution of porosity compared to AA6061 with ER 5356 welded joint confirmed by X-ray Ct-Scan. The decreasing of porosities and presence of very fine grains in weld region area with ER 5356 compared to ER 4043 will be discussed in term of microstructure analysis.