Traditional two-dimensional (2D) cell culture models of cancer cells do not truly recapitulate the disease in-vivo. Three-dimensional (3D) cell culture models are increasingly being developed and used in cancer research as they exhibit features closer to the cancer in-vivo conditions. Wnt/β-catenin and BMP are two well-studied signaling pathways whose aberrant activation has been involved in non-small cell lung cancer (NSCLC). We compared these two key signaling pathways in two NSCLC cell lines using 2D and 3D culture models. Protein expression in A549 and H460 cells, measured using Western Blotting, showed decreased expression of β-catenin in 3D cultures. RNA expression of Wnt/β-catenin pathway genes, measured using RT-PCR, showed increased expression of Cyclin-D1 and Axin2 in 3D cultures. RNA expression of BMP pathway genes showed increased expression of ID1. α-tubulin, a cytoskeletal protein that was used as our loading control, unexpectedly showed decreased protein and RNA expression in 3D samples. These results suggest that 3D cultures of NSCLC cells exhibit more adhesion and migration properties compared to 2D cell cultures.