Different environmental stresses, including salinity, can affect the photochemical efficiency and the antioxidant system of the plant. This work focused on the physiological, biochemical and molecular analysis of the photosynthetic apparatus and the antioxidant system in sugarcane under salt stress. Assays were conducted under controlled conditions (28 ^oC, 400 mmol m^-2 s^-1 photons). With this purpose, the Fv/Fm, qP and qNP of sugarcane cultivars RB72454 and CB4789 was analyzed by using a light modulated fluorimeter. Salt stress provoked no reduction of the variables Fv/Fm and qP, but qNP presented changes in the first hours of stress. In addition, chlorophyll levels were measured by using SPAD 502 analyzer to evaluate changes during the stress. A moderate reduction was verified in chlorophyll content after 72 hours of stress. Furthermore, nuclear genes related to the photosynthetic apparatus (PSII, PSI, Cytb6f and ATPase) were analyzed in macroarray assays with labeled cDNA obtained from leaves of control and stressed plants. Another effect during the salt stress is the increase in the production of reactive oxygen species during the photosynthesis. Plants are adequately protected by the presence of multiple antioxidative enzymes (SOD, CAT, APX and POX). To investigate the functions of these enzymes we studied the expression profile of respective genes in response to salt. A consequence of this oxidative stress was the transcript regulation in response to treatment, confirming the role of antioxidant enzymes during the salt stress. Beside, lipid peroxidation was determined by the malondialdehyde content. Among the cultivars, RB72454 presented the lowest peroxidation level, suggesting a higher tolerance to salt stress. Results allowed identifying differential expression of the photosynthetic and antioxidant system. Additionally, physiological and biochemical data showed a complex regulation of the sugarcane in response to salinity.