Novel pyrimido[5,4-d]pyrimidines were efficiently synthesized and evaluated for antibacterial activity against Mycobacterium tuberculosis strain H(37)Rv. This new structural class of compounds showed high activity against the bacilli. The activity depends on the substituents present in N-3 and C-8 of the pyrimido[5,4-d]pyrimidine core. Compounds having a 4-MeOC(6)H(4), a Ph or a 4-FC(6)H(4) group as the substituent on C-8 and a 4'-pyridinyl, a Ph or 2'-furyl group as the substituent on N-3 were active. The highest activity was registered for compounds having 4-FC(6)H(4) or 4-MeOC(6)H(4) as substituents in C-8 and a heteroaryl group as substituent in N-3. The new compounds showed high potency and promising antitubercular activity, as is the case of N-[8-[(4-fluorophenyl)amino]-4-iminopyrimido[5,4-d]pyrimidin-3(4H)-yl]isonicotinamide with an IC(90)=3.58 microg/mL, and should be regarded as new hits for further development as a novel class of Antimycobacterium tuberculosis agents.