Mycobacterium avium is an intracellular organism that can infect a number of cell types such as macrophages and epithelial cells. Each one of these cells represents a different environment that requires specific adaptation from the bacterium. The effect of uptake of M. avium and M. smegmatis by both human monocyte-derived macrophages in culture for 6 days, and HT-29 intestinal mucosal cell line on the bacterial synthesis of proteins were comparatively examined. Incorporation of [35S]-methionine by the bacterium was measured at 30 min, 2, 4, and 24 h after infection. Effect of the uptake by cells was compared with bacteria not exposed to cells and bacteria submitted to different stresses such as heat, hyperosmolarity and acid pH. Uptake of M. avium by macrophages triggered the synthesis of 93, 65, 55 and 33 kDa, among other proteins in the bacteria. Between 2 and 4 h of exposure to the intracellular millieu, a number of additional proteins have their synthesis up-regulated such as 39, 31, 43, 42, 61 and 70 kDa. In contrast, uptake by epithelial cells is associated with the up-regulation of 27, 65, 71 and 72 kDa proteins, among others. In this case, exposure to the intracellular environment was associated with expression of a number of proteins that do not vary with time. The results of this study suggest that regulation of the expression of proteins in M, avium varies according to the mammalian cell bacteria they are exposed to, and is influenced by the stage of intracellular infection.