Articular (medial femoral condyle) and auricular cartilage (anithelix) was compared as a cell source for the autologous joint repair. Cells isolated from five human cadaveric donors were cultured parallel in the monolayer cultures and in the 3D alginate hydrogel constructs for 1 week. Cell morphology was controlled by the fluorescent microscopy and gene expressions of type I collagen (COL1), type II collagen (COL2), aggrecan (AGR), versican (VER), and elastin (ELS) were analyzed by the real-time polymerase chain reaction. COL1 and ELS, predominant in the phenotype of auricular biopsy, were statistically lower in the articular biopsies. Even though COL2 and AGR decreased in monolayers of both cell sources, the dedifferentiation process affected auricular cells intensely. Cells embedded in the alginate hydrogel directly after the isolation did not exhibit the dedifferentiated phenotype. Additionally, COL1, COL2, AGR, and VER were comparable between the two sources. ELS however, remained higher in the auricular cells regardless of the culture type. The study indicates that auricular chondrocytes cultured in a 3D environment immediately after the isolation have a neo-cartilage potential for the articular surface reconstruction.