Methods, compounds and compositions are provided for inhibiting the growth of pathogenic microbes in vitro and of treatment of pathogenic bacterial infections, such as mycobacterial, Clostridium, Cryptosporidium and Helicobacter infections, in vivo using bicyclic nitroimidazole compounds of the formula (II): STR1 wherein R1 is hydrogen, halogen, loweralkyl, haloloweralkyl, cycloalkyl, heterocycle, substituted heterocycle and heterocyclicalkyl; X is oxygen, sulfur or NR2, where R2 is hydrogen, loweralkyl, aryl, cycloalkyl, heterocycle, substituted heterocycle, heterocyclicalkyl, COR3 or SO2 R4 CONR4 R5, where R3, R4 and R5 are independently selected from hydrogen, loweralkyl, aryl, alkylaryl, alkoxyalkyl, alkoxyaryl, alloxyalkoxyaryl, alkylheterocycle, and alkoxyheterocycle; n is 1, 2 or 3; Y and Z are independently selected from oxygen, CH2, CO, CR4 R5 or NR4, where R4 and R5 are as defined above; provided that when n is 2 or 3, the compounds of formula II can be additionally substituted as follows: STR2 wherein R6, R7, R8 and R9 are independently selected from hydrogen, loweralkyl, aryl, alkylaryl, alkoxyalkyl, alkoxyalkylaryl, alkoxyalkylheterocycle, alkylary2alkylaryl, alkylarylaryl, alkylcycloalkyl, alkoxyaryl, alkylheterocycle, and alkoxyheterocycle; and the pharmaceutically acceptable salts thereof.